Treatment of renal cell carcinoma

ABSTRACT

This disclosure provides methods for treating a subject afflicted with a tumor derived from a renal cell carcinoma. The methods comprise administering a first dose to a subject of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof, and administering a second dose to the subject, wherein the subject exhibited differential expression in one or more biomarker genes, e.g., CTLA-4, TIGIT, and/or PD-L2, following administration of the first dose.

Throughout this application, various publications are referenced in parentheses by author name and date, or by Patent No. or Patent Publication No. Full citations for these publications can be found at the end of the specification immediately preceding the claims. The disclosures of these publications are hereby incorporated in their entireties by reference into this application in order to more fully describe the state of the art as known to those skilled therein as of the date of the invention described and claimed herein. However, the citation of a reference herein should not be construed as an acknowledgement that such reference is prior art to the present invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 15/577,661, which is the national phase entity of International Application No. PCT/US2016/034875, filed May 27, 2016, which claims the priority benefit of U.S. Provisional Application Nos. 62/168,456, filed May 29, 2015, and 62/216,265, filed Sep. 9, 2015, each of which is incorporated by reference herein by reference in its entirety.

FIELD OF THE INVENTION

This invention relates to improving therapeutic efficacy of an anti-PD-1 antibody or an anti-PD-L1 in the treatment of a subject suffering from a tumor derived from a renal cell carcinoma (RCC).

BACKGROUND OF THE INVENTION

Human cancers harbor numerous genetic and epigenetic alterations, generating neoantigens potentially recognizable by the immune system (Sjoblom et al. (2006) Science 314:268-74). The adaptive immune system, comprised of T and B lymphocytes, has powerful anti-cancer potential, with a broad capacity and exquisite specificity to respond to diverse tumor antigens. Further, the immune system demonstrates considerable plasticity and a memory component. The successful harnessing of all these attributes of the adaptive immune system would make immunotherapy unique among all cancer treatment modalities.

Intensive efforts to develop specific immune checkpoint pathway inhibitors have begun to provide new immunotherapeutic approaches for treating cancer, including the development of an antibody (Ab), ipilimumab (YERVOY®), that binds to and inhibits CTLA-4 for the treatment of patients with advanced melanoma (YERVOY® FDA Full Prescribing Information, revised August 2015) and the development of antibodies such as nivolumab (OPDIVO®) and pembrolizumab (KEYTRUDA®) that bind specifically to the Programmed Death-1 (PD-1) receptor and block the inhibitory PD-1/PD-1 ligand pathway (see OPDIVO® FDA Full Prescribing Information, revised March 2015; KEYTRUDA® FDA Full Prescribing Information, revised June 2015).

PD-1 is a key immune checkpoint receptor expressed by activated T and B cells and mediates immunosuppression. PD-1 is a member of the CD28 family of receptors, which includes CD28, CTLA-4, ICOS, PD-1, and BTLA. Two cell surface glycoprotein ligands for PD-1 have been identified, Programmed Death Ligand-1 (PD-L1) and Programmed Death Ligand-2 (PD-L2), that are expressed on antigen-presenting cells as well as many human cancers and have been shown to downregulate T cell activation and cytokine secretion upon binding to PD-1.

Nivolumab (formerly designated 5C4, BMS-936558, MDX-1106, or ONO-4538), now approved as OPDIVO®, is a fully human IgG4 (S228P) PD-1 immune checkpoint inhibitor antibody that selectively prevents interaction with PD-1 ligands (PD-L1 and PD-L2), thereby blocking the down-regulation of antitumor T-cell functions (U.S. Pat. No. 8,008,449; Wang et al. (2014) Cancer Immunol Res. 2(9):846-56). Nivolumab has shown activity in a variety of advanced solid tumors.

Renal cancer (also known as kidney cancer) is a cancer that originates in the kidneys. The most common type of kidney cancer is renal cell carcinoma (RCC). RCC can often be cured by surgical resection if it is diagnosed and treated when still localized to the kidney and to the immediately surrounding tissue (Stage I), and radical resection is the accepted, often curative, therapy for Stage II as well as Stage III RCC. In contrast, when distant metastases are present (Stage IV), disease-free survival is poor. Moreover, the prognosis for any treated RCC patient with progressing, recurring, or relapsing disease is also poor, regardless of cell type or stage. Approximately 25%-30% of RCC patients have metastatic disease at diagnosis, and median survival for metastatic RCC is only about 24 months (Gupta et al. (2008) Cancer Treat Rev 34(3):193-205; NCCN GUIDELINES®, Version 3.2014—Kidney Cancer; Heng et al. (2009) J Clin Oncol. 27:5794-9). Responses to cytotoxic chemotherapy generally have not exceeded 10% for any regimen that has been studied in adequate numbers of patients.

SUMMARY OF THE INVENTION

The present disclosure relates to a method for treating a subject afflicted with a tumor derived from a RCC comprising: (i) administering to the subject a first dose of an antibody or an antigen-binding portion thereof that binds specifically to PD-1 or PD-L1 and inhibits PD-1 activity (“anti-PD-1 antibody or antigen-binding portion thereof”) or PD-L1 activity (“anti-PD-L1 antibody or antigen-binding portion thereof”), respectively; and (ii) administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof to the subject wherein after the administration of the first dose, the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof.

The present disclosure also relates to a method for treating a subject afflicted with a tumor derived from an RCC comprising administering, to the subject who exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after administration of a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In one embodiment, the present disclosure relates to a method of treating a subject afflicted with a tumor derived from an RCC comprising: (i) determining an expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in a sample of the subject after the subject is administered with a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, wherein the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after the administration of the first dose and (ii) administering to the subject a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In another embodiment, the present disclosure relates to a method of treating a subject afflicted with a tumor derived from an RCC comprising: (i) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, (ii) determining an expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in a sample of the subject after (i), wherein the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof compared to the expression level prior to (i); and (ii) administering to the subject a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In other embodiments, the present disclosure relates to a method for identifying a subject afflicted with an RCC who is suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising measuring an expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in a sample of the subject, wherein the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after administration of a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof and wherein the subject is administered a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In some embodiments, the present disclosure relates to a method for identifying a subject afflicted with an RCC suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising: (i) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, and (ii) measuring an expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in a sample of the subject after (i), wherein the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof compared to the expression level prior to (i); wherein the subject is administered a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In certain embodiments, the present disclosure relates to a kit for treating a subject afflicted with a tumor derived from an RCC, the kit comprising: (a) an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof (b) instructions for determining differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after administration of a first dose of the anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof and for administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof if the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof. In certain embodiments, the kit further comprises an agent to determine differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof prior to administering the second dose.

In certain embodiments, the differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in the subject is relative to the expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 before the administration of the first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof (i.e., at baseline). In one embodiment, the differential expression is an increased expression after the administration.

In other embodiments, the differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof is relative to the expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 in non-responders. In yet other embodiments, the differential expression in the subject is a higher expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2 or any combination thereof in one or more non-responders.

In certain embodiments, the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, PD-L2, or both after the administration of the first dose.

In some embodiments, after the administration of the first dose and/or the second dose, the subject further exhibits a characteristic selected from the group consisting of: (i) an increased expression of one or more serum markers of Interferon-γ activation; (ii) an increased tumor gene expression; (iii) a decreased clonality of T cell Receptor in serum; (iv) an increased T cell count in the tumor; and (v) any combination thereof.

In some embodiments, the differential expression is measured by comparing the expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof prior to the administration of the first dose and after the administration of the first dose. In other embodiments, the differential expression is measured by comparing the expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof in responding subjects (“responders”) and in non-responding (“non-responders”) subjects. In certain embodiments, the expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof is a protein expression measured by an immunohistochemistry, an ELISA, a western blot, a protein array, or any combination thereof. In another embodiment, the expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof is a nucleotide expression measured by an in situ hybridization, a DNA or RNA array or nucleotide hybridization technique, a tumor sequencing technique, a quantitative polymerase chain reaction (PCR), or any combination thereof. In certain embodiments, the tumor further expresses PD-L1.

In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof cross-competes with nivolumab for binding to human PD-1. In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is a chimeric, humanized, or human monoclonal antibody, or a portion thereof. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof comprises a heavy chain constant region which is of a human IgG1 or IgG4 isotype. In one particular embodiment, the anti-PD-1 antibody is nivolumab. In another embodiment, the anti-PD-1 antibody is pembrolizumab.

In other embodiments, the anti-PD-L1 antibody or antigen-binding portion thereof cross-competes with BMS-936559, MPDL3280A, MEDI4736, or MSB0010718C for binding to human PD-L1. In certain embodiments, the anti-PD-L1 antibody or antigen-binding portion thereof is a chimeric, humanized, or human monoclonal antibody, or a portion thereof. In some embodiments, the anti-PD-L1 antibody or antigen-binding portion thereof comprises a heavy chain constant region which is of a human IgG1 or IgG4 isotype. In one embodiment, the anti-PD-L1 antibody is BMS-936559. In another embodiment, the anti-PD-L1 antibody is MPDL3280A. In a further embodiment, the anti-PD-L1 antibody is MEDI4736. In another embodiment, the anti-PD-L1 antibody is MSB0010718C.

In certain embodiments, the first dose is a therapeutic dose and the second dose is a therapeutic dose. In other embodiments, the first dose is a subtherapeutic dose and the second dose is a therapeutic dose. In some embodiments, the first dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg or at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight. In some embodiments, the second dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg or at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight. In one particular embodiment, the first dose is administered at a dose of at least about 3 mg/kg body weight or 240 mg once about every 2 weeks.

In some embodiments, the subject is administered at least two doses, at least three doses, at least four doses, at least five doses, at least six doses, at least seven doses, at least eight doses, at least nine doses, at least ten doses, at least 12 doses, at least 20 doses, or at least 30 doses prior to measuring the increased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof. In certain embodiments, the anti-PD-1 antibody or antigen-binding portion or the anti-PD-L1 antibody or antigen-binding portion thereof is administered for as long as a clinical benefit is observed or until unmanageable toxicity or disease progression occurs.

In some embodiments, the subject shows an increase in the number of CD4+ tumor associated lymphocytes in the tumor, an increase in the number of CD8+ tumor associated lymphocytes in the tumor, an increased expression level of chemokine (C-X-C motif) ligand-9 (CXCL9) in a serum, an increased expression level of CXCL10 in a serum, or any combination thereof after the administration of the second dose.

In certain embodiments, the subject exhibits an overall survival of at least about 18 months, at least about 19 months, at least about 20 months, at least about 21 months, at least about 22 months, at least about 23 months, at least about 2 years, at least about 3 years, at least about 4 years, or at least about 5 years after the administration.

In some embodiments, the method further comprises administering one or more additional anti-cancer agents. In certain embodiments, the anti-cancer agent is selected from the group consisting of an antibody or antigen-binding portion thereof that binds specifically to CTLA-4 (“anti-CTLA-4 antibody or antigen-binding portion thereof”) and inhibits CTLA-4 activity, a chemotherapy, a platinum-based doublet chemotherapy, a tyrosine kinase inhibitor, an anti-VEGF inhibitor, or any combination thereof. In a particular embodiment, the anti-cancer agent is an antibody or antigen-binding portion thereof that binds specifically to CTLA-4 and inhibits CTLA-4 activity. In one embodiment, the anti-cancer agent is ipilimumab.

In some aspects, the invention is directed to a method of identifying a subject afflicted with a tumor who is suitable for an anti-PD-1 antibody or an anti-PD-L1 antibody therapy comprising measuring an expression level of one or more genes selected from the group consisting of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject prior to the anti-PD-1 antibody or anti-PD-L1 antibody therapy. In some embodiments, the method further comprises administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to a method for identifying a subject afflicted with a tumor who is suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising measuring an expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject prior to the anti-PD-1 antibody or anti-PD-L1 antibody therapy, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, and wherein the subject is administered a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to a method for treating a subject afflicted with a tumor comprising administering, to the subject who exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to method for treating a subject afflicted with a tumor comprising administering a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7.

In another aspect, the invention is directed to method for treating a subject afflicted with a tumor comprising: (i) measuring an expression level of one or more genes selected from the group consisting of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, and (ii) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein the subject exhibits an increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7.

In another aspect, the invention is directed to a method of treating a subject afflicted with a tumor comprising: (i) determining an expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7; and (ii) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic of a study design and objectives directed to treatment of mRCC. Abbreviations include Karnofsky performance score (KPS), metastatic renal cell carcinoma (mRCC), ratio (R), intravenously (IV), every three weeks (Q3W), and complete response (CR).

FIG. 2 shows a consort diagram of the study outlined in FIG. 1. FIG. 2 summarizes the patient outcomes for each of Arms 1, 2, 3, and 4, including the occurrence rate of drug related adverse events (AEs).

FIG. 3 shows a graphical representation of the overall survival (OS) of patients treated with 0.3 mg/kg (triangles; Arm 1), 2 mg/kg (open circles; Arm 2), or 10 mg/kg (closed circles; Arm 3) body weight nivolumab and naïve patients treated with 10 mg/kg body weight nivolumab (squares; Arm 4). OS rates are shown with their corresponding 95% confidence interval (CI) values at 12 months and 24 months. The number of events per patient and the median OS (95% CI) for each treatment group are also shown. OS point estimates were derived from Kaplan-Meier analyses, and 95% CIs were derived using Greenwood's formula. “Naïve” subjects have not received any prior therapy, as described below. Point estimates are derived from Kaplan-Meier analyses. 95% CLs are derived from Greenwood's formula. NR means not reached.

FIGS. 4A-4D show images of immunohistochemistry (IHC) for CD3+, CD4+, and CD8+ cells at baseline and cycle 2 day 8 (C2D8) in sample tumor tissue. Scale bars are denoted on the images. FIG. 4A shows CD3 and CD8 staining at baseline. FIG. 4B shows CD3 and CD8 staining from biopsied tissue collected at C2D8 of nivolumab treatment. FIG. 4C shows CD4, FoxP3, and CD3 staining at baseline. FIG. 4D shows CD4, FoxP3, and CD3 staining from biopsied tissue collected at C2D8 of nivolumab treatment. FIGS. 4E-4G show the changes from baseline percentage of cells that are CD3+(FIG. 4E), CD4+(FIG. 4F), or CD8+(FIG. 4G) in tumor biopsies. Data are included for patients with IHC data at both baseline and cycle 2 day 8 in all treatment groups combined (N=36) (FIGS. 4E-4G).

FIG. 5A shows scatter-plot matrices of change from baseline (CFB) of CD3+v. CD4+ cell percentages among the 36 patients. FIG. 5B shows scatter-plot matrices of change from baseline (CFB) of CD3+v. CD8+ cell percentages among the 36 patients. FIG. 5C shows scatter-plot matrices of change from baseline (CFB) of CD4+v. CD8+ cell percentages among the 36 patients. FIGS. 5D, 5E, and 5F give kernel density estimates and histograms summarizing the univariate distributions for the individual cell-type percentages for CD3+, CD4+, and CD8+ cells, respectively.

FIGS. 5G, 5H, and 5J show expression levels for genes CD3D (915_at), CD8A (925_at) and CD4 (920_at) in tumor biopsies, respectively. Values presented are least-squares means (LSM) of robust multi-array average (RMA) intensity for the treatment group and time point indicated. Data were obtained from an extended linear model that included fixed effects of treatment group, time on study, process batch and sex (the latter because women were not equally represented in samples from each trial treatment group) as categorical variables, and treatment-by-time on study interactions, and that modeled within-patient correlations by a spatial exponential structure with Euclidean distance. Error bars indicate 95% CIs.

FIGS. 6A-6D show graphical representations of the receptor occupancy for total lymphocytes in sample collected from previously treated subjects receiving 0.3 mg/kg (FIG. 6A; Arm 1), 2 mg/kg (FIG. 6B; Arm 2), and 10 mg/kg (FIG. 6C; Arm 3) nivolumab and treatment-naïve subjects receiving 10 mg/kg nivolumab (FIG. 6D; Arm 4). Light gray lines represent individual time profiles; bold lines connect medians at individual time points. The x-axis shows the time-point, wherein, e.g., “C1D1 0 h” indicates that the sample measured was collected at cycle 1, day 1, 0 hours. The y-axis shows the percentage of receptor occupancy.

FIG. 7A is a heat map representing microarray expression data, which shows the fold change of the expression level in tumor biopsies of 43 regulated transcripts (>1.3 fold, p<0.01) that are specifically associated with either the lymphoid or myeloid immune lineage. Within the lymphoid lineage, 10 transcripts indicated are specific to T cells. Data are included from 42 patients with measures at both time points, separated by their previous treatment status. Genes, listed on the right, labeled by a (**) are members of interferon-regulated transcription modules collated by the BRi2 consortium (Chaussabel et al. (2008) Immunity 29:150-64). Markers of immune cytolytic activity are labeled by a (*).

FIG. 7B is a schematic representation of the components of antigen presentation regulated by PD-1.

FIG. 7C is a heat map representing microarray expression data, which show the fold change of 30 transcripts in peripheral blood associated with immune lineages and significantly regulated (>1.2-fold, p<0.01) in all treatment groups at cycle 1 day 2. Data are included from 70 patients with measures at both time points, separated by treatment group. Genes labeled by a (*) are members of interferon-regulated transcription modules collated by the BRi2 consortium (Chaussabel et al. (2008) Immunity 29:150-64).

FIG. 8A and FIG. 8B are heat maps representing microarray expression data, which show relative gene expression in subjects pre-treatment and on-treatment, respectively. In FIG. 8A, the upper panel shows 311 transcripts that were found to be differentially expressed (P<0.01, >1.3× difference, and a false discovery rate <16%) at baseline in patients who displayed a greater than 20% reduction in tumor burden as compared to those patients with a less than 20% reduction in tumor burden. In FIG. 8B, the upper panel shows 779 genes that were found to be differentially expressed (P<0.01, >1.3× difference, and a false discovery rate <16%) on treatment, as compared to pre-treatment, in patients who displayed a greater than or equal to 20% reduction in tumor burden as compared to those patients with a less than 20% reduction. Shading shows the Z score for each gene, from −2 to +2 standard deviations (SD). The lower panels of both FIG. 8A and FIG. 8B are graphical representations of the best change (A) in tumor burden (%) for each patient in the upper panel, with the horizontal dashed line marking the 20% reduction in tumor burden, and the vertical line separating those subjects with less than 20% reduction in tumor burden from those with more than 20% reduction in tumor burden. FIGS. 8C-8E show the relative expressions of three immune checkpoint genes, CTLA-4 (FIG. 8C), TIGIT (FIG. 8D), and PD-L2 (FIG. 8E) on-treatment as compared to baseline. Each circle represents the robust multi-array average (RMA) signal (e.g., an indicator of relative expression) of a single subject, wherein the white circles represent subjects exhibiting a less than 20% reduction in tumor burden, and wherein the grey circles represent subjects exhibiting a greater than or equal to 20% reduction in tumor burden (FIGS. 8C-8E). Vertical bars indicate the mean and 95% confidence interval (CI). Significance in FIGS. 8C-8E is shown as a p value above each panel. Data shown in FIGS. 8C-8E are largest reduction in tumor burden from baseline.

FIGS. 9A-9H and 9J-9M show the effect of nivolumab on chemokine markers. FIGS. 9A and 9B illustrate the relationship between serum soluble factors and overall survival at baseline (FIG. 8F) and the corresponding changes from baseline (FIG. 8G). The hazard ratio (HR) in FIGS. 8F and 8G is shown on the right, which compares an increment equivalent to the 75^(th) percentile (Q3) of the soluble factor to the 25^(th) percentile (Q1), with the 95% confidence interval in parentheses. The log hazard ratio is indicated on the x-axis of each of FIGS. 8F and 8G. All analyses are exploratory, not confirmatory. The Cox proportional hazards model used accounts for dose and naïve/previously treated status. The sample size ranged from 74-90.

FIGS. 9B and 9C are graphical representations of the fold changes from baseline at cycle 2 day 8 in serum concentrations of CXCL9 (FIG. 9C) and CXCL10 (FIG. 9D) in all treatment groups (N=83). Both the x- and y-axes are on the log base-2 scale. Each circle represents the fold change from baseline measured in a single subject.

FIG. 9F and FIG. 9G are scatter plot matrices of fold changes from baseline (log base-2 scale) in CXCL10 v. CXCL9 (FIG. 9F) and CXCL9 v. CXCL10 (FIG. 9G) among 83 patients who had serum data at baseline and cycle 2 day 8. FIGS. 9E and 9H give kernel density estimates and histograms summarizing the univariate distributions of CXCL9 (FIG. 9E) and CXCL10 (FIG. 9H), individually.

FIGS. 9J and 9K show graphical representations of gene expression levels for CXCL9 (4283_at) (FIG. 9J) and CXCL10 (3627_at) (FIG. 9K) in fresh tumor tissue samples taken at baseline and at cycle 2 day 9 (C2D8). Values presented are least squares means of RMA intensity for the treatment group and time point indicated (FIGS. 9J and 9K). Error bars indicate 95% CIs (FIGS. 9J and 9K). Data is presented for samples collected from subjects in the 0.3 (solid line), 2 (squares), and 10 (open circles) mg/kg nivolumab treatment groups and the 10 mg/kg (naïve) nivolumab treatment group (closed circles) (FIGS. 9J and 9K).

FIGS. 9L and 9M show graphical representations of the relationship between serum concentration and biopsy gene expression for CXCL9 (FIG. 9L) and CXCL10 (FIG. 9M). Values presented are least squares means of RMA intensity for the treatment group and the serum concentration (pg/ml) (FIGS. 9L and 9M). The data for individual subjects are indicates by open circles, with a trend line superimposed (FIGS. 9L and 9M).

FIG. 10A shows a schematic of T cell receptor (TCR) recombination as exploited by TCR sequencing to measure T cell clonality, including the process of T cell V(D)J recombination, whereby an Ig/TCR transcript is created by expression of one V domain, the D domain, and one J domain. FIG. 10B shows representative drawings of a high clonality TCR repertoire (FIG. 10B); FIG. 10C shows representative drawings of a low clonality TCR repertoire.

FIGS. 10D-10F show graphical representations of a univariate Cox proportional hazards analyses of pre-treatment and on treatment tumor cell frequency (FIG. 10D), tumor clonality (FIG. 10E), and blood clonality (FIG. 10F). Log hazard ratio (HR) is shown on the x-axis with relative overall survival (OS). To the right of each of FIGS. 10D-10F is the corresponding HR (95% confidence interval [CI]).

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to methods of enhancing the clinical efficacy of an anti-PD-1 or anti-PD-L1 immunotherapy in the treatment of a subject suffering from a tumor derived from a renal cell carcinoma (RCC). In particular, the invention includes methods for treating mRCC in a subject comprising administering to the subject a dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof, wherein the subject is determined to have differential expression of one or more gene, e.g., CTLA-4, TIGIT, PD-L2, or any combination thereof, during the anti-PD-1 antibody or anti-PD-L1 antibody therapy. In other embodiments, the invention includes methods for treating an RCC in a subject comprising administering to the subject a dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof, wherein the subject is determined to have differential expression of one or more gene, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof, during the anti-PD-1 antibody or anti-PD-L1 antibody therapy.

I. Terms

In order that the present disclosure can be more readily understood, certain terms are first defined. As used in this application, except as otherwise expressly provided herein, each of the following terms shall have the meaning set forth below. Additional definitions are set forth throughout the application.

The term “and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

As described herein, any concentration range, percentage range, ratio range or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.

It is understood that wherever aspects are described herein with the language “comprising,” otherwise analogous aspects described in terms of “consisting of” and/or “consisting essentially of” are also provided.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure is related. For example, the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei-Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 3rd ed., 1999, Academic Press; and the Oxford Dictionary Of Biochemistry And Molecular Biology, Revised, 2000, Oxford University Press, provide one of skill with a general dictionary of many of the terms used in this disclosure.

Units, prefixes, and symbols are denoted in their Systeme International de Unites (SI) accepted form. Numeric ranges are inclusive of the numbers defining the range. The headings provided herein are not limitations of the various aspects of the disclosure, which can be had by reference to the specification as a whole. Accordingly, the terms defined immediately below are more fully defined by reference to the specification in its entirety.

“Administering” refers to the physical introduction of a composition comprising a therapeutic agent to a subject, using any of the various methods and delivery systems known to those skilled in the art. Routes of administration for the anti-PD-1 antibody and/or the anti-PD-L1 antibody include intravenous, intramuscular, subcutaneous, intraperitoneal, spinal or other parenteral routes of administration, for example by injection or infusion. The phrase “parenteral administration” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intralymphatic, intralesional, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural and intrasternal injection and infusion, as well as in vivo electroporation. Non-parenteral routes include a topical, epidermal or mucosal route of administration, for example, orally, intranasally, vaginally, rectally, sublingually or topically. Administering can also be performed, for example, once, a plurality of times, and/or over one or more extended periods.

An “adverse event” (AE) as used herein is any unfavorable and generally unintended or undesirable sign (including an abnormal laboratory finding), symptom, or disease associated with the use of a medical treatment. For example, an adverse event can be associated with activation of the immune system or expansion of immune system cells (e.g., T cells) in response to a treatment. A medical treatment can have one or more associated AEs and each AE can have the same or different level of severity. Reference to methods capable of “altering adverse events” means a treatment regime that decreases the incidence and/or severity of one or more AEs associated with the use of a different treatment regime.

An “antibody” (Ab) shall include, without limitation, a glycoprotein immunoglobulin which binds specifically to an antigen and comprises at least two heavy (H) chains and two light (L) chains interconnected by disulfide bonds, or an antigen-binding portion thereof. Each H chain comprises a heavy chain variable region (abbreviated herein as V_(H)) and a heavy chain constant region. The heavy chain constant region comprises three constant domains, C_(H1), C_(H2) and C_(H3). Each light chain comprises a light chain variable region (abbreviated herein as V_(L)) and a light chain constant region. The light chain constant region is comprises one constant domain, C_(L). The V_(H) and V_(L) regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FR). Each V_(H) and V_(L) comprises three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies can mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1q) of the classical complement system. In some embodiments, the constant region of the antibodies can be substituted or mutated to alter the effector function.

An immunoglobulin can derive from any of the commonly known isotypes, including but not limited to IgA, secretory IgA, IgG and IgM. IgG subclasses are also well known to those in the art and include but are not limited to human IgG1, IgG2, IgG3 and IgG4. “Isotype” refers to the antibody class or subclass (e.g., IgM or IgG1) that is encoded by the heavy chain constant region genes. The term “antibody” includes, by way of example, both naturally occurring and non-naturally occurring antibodies; monoclonal and polyclonal Abs; chimeric and humanized antibodies; human or nonhuman antibodies; wholly synthetic antibodies; and single chain antibodies. A nonhuman antibody can be humanized by recombinant methods to reduce its immunogenicity in man. Where not expressly stated, and unless the context indicates otherwise, the term “antibody” also includes an antigen-binding fragment or an antigen-binding portion of any of the aforementioned immunoglobulins, and includes a monovalent and a divalent fragment or portion, and a single chain antibody.

An “isolated antibody” refers to an antibody that is substantially free of other antibodies having different antigenic specificities (e.g., an isolated antibody that binds specifically to PD-1 is substantially free of antibodies that bind specifically to antigens other than PD-1). An isolated antibody that binds specifically to PD-1 or PD-L1 can, however, have cross-reactivity to other antigens, such as PD-1 or PD-L1 molecules, respectively, from different species. Moreover, an isolated antibody can be substantially free of other cellular material and/or chemicals.

The term “monoclonal antibody” (“mAb”) refers to a non-naturally occurring preparation of antibody molecules of single molecular composition, i.e., antibody molecules whose primary sequences are essentially identical, and which exhibits a single binding specificity and affinity for a particular epitope. A mAb is an example of an isolated antibody. MAbs can be produced by hybridoma, recombinant, transgenic or other techniques known to those skilled in the art.

A “human antibody” (HuAb) or a “human monoclonal antibody” (HuMAb) refers to an antibody having variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences. Furthermore, if the antibody contains a constant region, the constant region also is derived from human germline immunoglobulin sequences. The human antibodies of the invention can include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo). However, the term “human antibody,” as used herein, is not intended to include antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences. The terms “human” antibodies and “fully human” antibodies and are used synonymously.

A “humanized antibody” refers to an antibody in which some, most or all of the amino acids outside the CDR domains of a non-human antibody are replaced with corresponding amino acids derived from human immunoglobulins. In one embodiment of a humanized form of an antibody, some, most, or all of the amino acids outside the CDR domains have been replaced with amino acids from human immunoglobulins, whereas some, most or all amino acids within one or more CDR regions are unchanged. Small additions, deletions, insertions, substitutions or modifications of amino acids are permissible as long as they do not abrogate the ability of the antibody to bind to a particular antigen. A “humanized” antibody retains an antigenic specificity similar to that of the original antibody.

A “chimeric antibody” refers to an antibody in which the variable regions are derived from one species and the constant regions are derived from another species, such as an antibody in which the variable regions are derived from a mouse antibody and the constant regions are derived from a human antibody.

An “anti-antigen” antibody refers to an antibody that binds specifically to the antigen. For example, an anti-PD-1 antibody binds specifically to PD-1, an anti-PD-L1 antibody binds specifically to PD-L1, and an anti-CTLA-4 antibody binds specifically to CTLA-4.

An “antigen-binding portion” of an antibody (also called an “antigen-binding fragment”) refers to one or more fragments of an antibody that retain the ability to bind specifically to the antigen bound by the whole antibody.

A “cancer” refers to a broad group of various diseases characterized by the uncontrolled growth of abnormal cells in the body. Unregulated cell division and growth results in the formation of malignant tumors that invade neighboring tissues and can also metastasize to distant parts of the body through the lymphatic system or bloodstream. A “cancer” or “cancer tissue” can include a tumor. In some embodiments, the cancer is a kidney cancer.

The vast majority of patients suffering from a kidney cancer, about 90% of kidney cancer patients, have an RCC, also referred to as a renal cell adenocarcinoma. RCC accounts for about 3% of all cancers in the United States, and an estimated 63,920 patients will be diagnosed with renal cancer and 13,860 will die of the disease in the U.S. in 2014 (Siegel et al. (2014) CA Cancer J Clin 64(1):9-29). Metastatic disease is found in about 30% of subjects at diagnosis.

RCC includes several subtypes with physiological and clinical differences. The most common RCC subtypes include clear cell RCC (about 70% of all RCCs), papillary RCC or chromophilic RCC (about 10% of all RCCs), and chromophobe RCC (about 5% of all RCCs). The remaining subtypes include, but are not limited to, oncocytoma, collecting duct RCC, multilocular cystic RCC, medullary carcinoma, mucinous tubular and spindle carcinoma, and neuroblastoma-associated RCC, as well as unclassified RCCs, which don't fit into one group or comprise more than one type of subtype. In one particular embodiment, the mRCC is a clear cell RCC or comprises a clear-cell component. In other embodiments, the renal cancer is an advanced, metastatic, and/or refractory cancer. In certain embodiments, the RCC is a metastatic (mRCC). Kidney cancers can also include less common forms, including, but not limited to, transitional cell carcinomas (about 5-10% of kidney cancer patients), Wilms tumors or nephroblastomas (very rare in adults, but accounts for 5% of all cancers in children), and renal sarcomas (less than 1% of kidney cancer patients).

“Cytotoxic T-Lymphocyte Antigen-4” (CTLA-4) refers to an immunoinhibitory receptor belonging to the CD28 family. CTLA-4 is expressed exclusively on T cells in vivo, and binds to two ligands, CD80 and CD86 (also called B7-1 and B7-2, respectively). The term “CTLA-4” as used herein includes human CTLA-4 (hCTLA-4), variants, isoforms, and species homologs of hCTLA-4, and analogs having at least one common epitope with hCTLA-4. The complete hCTLA-4 sequence can be found under GenBank Accession No. AAB59385.

The term “immunotherapy” refers to the treatment of a subject afflicted with, or at risk of contracting or suffering a recurrence of, a disease by a method comprising inducing, enhancing, suppressing or otherwise modifying an immune response.

“Treatment” or “therapy” of a subject refers to any type of intervention or process performed on, or the administration of an active agent to, the subject with the objective of reversing, alleviating, ameliorating, inhibiting, slowing down or preventing the onset, progression, development, severity or recurrence of a symptom, complication or condition, or biochemical indicia associated with a disease.

“PD-L1 positive” as used herein can be interchangeably used with “PD-L1 expression of at least about 5%.” PD-L1 expression can be measured by any methods known in the art. In some embodiments, the PD-L1 expression is measured by an automated IHC. A PD-L1 positive tumor can thus have at least about 5%, at least about 10%, or at least about 20% of tumor cells expressing PD-L1 as measured by an automated IHC. In certain embodiments, “PD-L1 positive” means that there are at least 100 cells that express PD-L1 on the surface of the cells.

“Programmed Death-1” (PD-1) refers to an immunoinhibitory receptor belonging to the CD28 family. PD-1 is expressed predominantly on previously activated T cells in vivo, and binds to two ligands, PD-L1 and PD-L2. The term “PD-1” as used herein includes human PD-1 (hPD-1), variants, isoforms, and species homologs of hPD-1, and analogs having at least one common epitope with hPD-1. The complete hPD-1 sequence can be found under GenBank Accession No. U64863.

“Programmed Death Ligand-1” (PD-L1; B7 homolog-1; B7-H1; or CD274) and “Programmed Death Ligand-2” (PD-L2; B7-DC; or CD273) are two cell surface glycoprotein ligands for PD-1 that downregulate T-cell activation and cytokine secretion upon binding to PD-1. The terms “PD-L1” and “PD-L2” as used herein include human PD-L1 (hPD-L1) and human PD-L2 (hPD-L2) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hPD-L1 and/or hPD-L2. The complete hPD-L1 sequence can be found under GenBank Accession No. Q9NZQ7. The complete hPD-L2 sequence can be found under GenBank Accession No. NP_079515.

“T-cell Immunoreceptor with Ig and ITIM Domains” (“TIGIT”; V-Set and Immunoglobulin Domain-Containing Protein-9 (VSIG9); and VSTM3) refers to a protein that binds the poliovirus receptor (PVR), causing increased secretion of interleukin-10 (IL10) and decreased secretion of IL12B and suppresses T-cell activation by promoting the generation of mature immunoregulatory dendritic cells. TIGIT is expressed on various types of T cells including follicular B helper T cells (TFH), and it is also believed to facilitate the interaction between TFH and dendritic cells to regulate T cell-dependent B cell responses. The term “TIGIT” as used herein refers to the human TIGIT (hTIGIT) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hTIGIT. The complete hTIGIT sequence can be found under GenBank Accession No. NP 776160.

“MHC class I polypeptide-related sequence B” (“MICB”; PERB11.2) refers to a protein that is a ligand for the NKG2D type II receptor (KLRK1). NKG2D recognizes the induced-self proteins MICA, MICB, RAET1E/ULBP4, RAET1G/ULBP5, RAET1H/ULBP2, RAET1/ULBP1, RAET1L/ULBP6, and RAET1N/ULBP3, which appear on the surface of stressed, malignant transformed, and infected cells. Binding of these ligands activates the cytolytic response of natural killer (NK) cells, CD8 αβ T cells, and γδ T cells which express the NKG2D receptor. The term “MICB” as used herein refers to the human MICB (hMICB) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hMICB. The complete hMICB sequence can be found under GenBank Accession No. NP_005922.

“Natural killer cell granule protein 7” (“NKG7”; GIG1; GMP-17; p15-TIA-1) refers to a protein that is expressed in natural killer cells and T cells. The term “NKG7” as used herein refers to the human NKG7 (h NKG7) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hNKG7. The complete hNKG7 sequence can be found under GenBank Accession No. NP_005592.

“Poliovirus receptor related immunoglobulin domain containing” (“PVRIG”; CD112R) refers to a protein from an mRNA that is preferentially transcribed in T lymphocytes and NK cells. Like TIGIT, PVRIG is a receptor for CD112, and both receptors are considered suppressive for T cell activation. The term “PVRIG” as used herein refers to the human PVRIG (hPVRIG) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hPVRIG. The complete hPVRIG sequence can be found under GenBank Accession No. NP 076975.

“Spi-1 proto-oncogene” (“SPI1”; OF; PU.1; SFPI1; SPI-1; SPI-A) refers to a protein that is a transcription factor that activates gene expression during myeloid and B-lymphoid cell development. SPI1 expression is present at high levels in mature myeloid cells. Myeloid leukaemias are associated with downregulated activity of myeloid transcription factors, and mutations in the SPI1 gene were identified in 7% of patients with AML in one study. The term “SPI1” as used herein refers to the human SPI1 (hSPI1) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hSPI1. The complete hSPI1 sequence can be found under GenBank Accession No. NP 001074016.

“C-type lectin domain family 2 member B” (“CLEC2B”; AICL; IFNRG1; CLECSF2; HP10085) refers to a protein that is a myeloid-specific activating receptor that binds NKp80 (KLRF1) on natural killer (NK) cells. NKp80-CLEC2B interactions may contribute to the initiation and maintenance of immune responses at sites of inflammation. The term “CLEC2B” as used herein refers to the human CLEC2B (hCLEC2B) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hCLEC2B. The complete hCLEC2B sequence can be found under GenBank Accession No. NP 005118.

“CD244 molecule” (“CD244”; 2B4; NAIL; Nmrk; NKR2B4; SLAMF4) refers to a protein expressed on natural killer (NK) cells (and some T cells) that mediates non-major histocompatibility complex restricted killing. The interaction between NK-cell and target cells via this receptor is thought to modulate NK-cell cytolytic activity. The term “CD244” as used herein refers to the human CD244 (hCD244) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hCD244. The complete hCD244 sequence can be found under GenBank Accession No. NP_057466.

“Natural killer cell triggering receptor” (“NKTR”; p104) refers to a protein present on the surface of natural killer cells that facilitates their binding to targets. Its expression is regulated by IL2 activation of the cells. The term “NKTR” as used herein refers to the human NKTR (hNKTR) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hNKTR. The complete hNKTR sequence can be found under GenBank Accession No. NP_005376.

“Tumor necrosis factor superfamily member 13b” (“TNFSF13B”; DTL; BAFF; BLYS; CD257; TALL1; THANK; ZTNF4; TALL-1; TNLG7A; TNFSF20) refers to a protein ligand for receptors TNFRSF13B/TACI, TNFRSF17/BCMA, and TNFRSF13C/BAFFR. This cytokine is expressed in B cell lineage cells, and acts as a potent B cell activator. It has been also shown to play an important role in the proliferation and differentiation of B cells. The term “TNFSF13B” as used herein refers to the human TNFSF13B (hTNFSF13B) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hTNFSF13B. The complete hTNFSF13B sequence can be found under GenBank Accession No. NP_006564.

“Tumor necrosis factor receptor superfamily member 14” (“TNFRSF14”; TR2; ATAR; HVEA; HVEM; CD270; LIGHTR) refers to a protein that functions in signal transduction pathways that activate inflammatory and inhibitory T-cell immune response. The term “TNFRSF14” as used herein refers to the human TNFRSF14 (hTNFRSF14) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with hTNFRSF14. The complete hTNFRSF14 sequence can be found under GenBank Accession No. NP_003811.

“Tumor necrosis factor superfamily member 8” (“TNFSF8”; CD153; CD30 ligand (CD30L, CD30LG)) refers to a protein that is a cytokine with pleiotropic biologic activities. TNFSF8 is a ligand for TNFRSF8/CD30, which is a cell surface antigen and a marker for Hodgkin lymphoma and related hematologic malignancies. The engagement of this cytokine expressed on B cell surface plays an inhibitory role in modulating Ig class switch. The term “TNFSF8” as used herein refers to the human TNFSF8 (h TNFSF8) and variants, isoforms, and species homologs thereof, and analogs having at least one common epitope with h TNFSF8. The complete hTNFSF8 sequences can be found under GenBank Accession Nos. NP_001235.1 and NP_001239219.1.

A “subject” includes any human or nonhuman animal. The term “nonhuman animal” includes, but is not limited to, vertebrates such as nonhuman primates, sheep, dogs, and rodents such as mice, rats and guinea pigs. In some embodiments, the subject is a human. The terms, “subject” and “patient” are used interchangeably herein. A “responding” subject, or a “responder,” is a subject who has responded to a treatment, e.g., a subject who has responded to a treatment with an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof. A “non-responding” subject, or a “non-responder,” is a subject who has not responded to a treatment, e.g., a subject who has not responded to a treatment with an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

A “therapeutically effective amount” or “therapeutically effective dosage” of a drug or therapeutic agent is any amount of the drug that, when used alone or in combination with another therapeutic agent, protects a subject against the onset of a disease or promotes disease regression evidenced by a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction. A “subtherapeutic amount” as used herein refers to a dosage of a drug or therapeutic agent that is significantly lower than the approved dosage. The ability of a therapeutic agent to promote disease regression can be evaluated using a variety of methods known to the skilled practitioner, such as in human subjects during clinical trials, in animal model systems predictive of efficacy in humans, or by assaying the activity of the agent in in vitro assays.

A subject may be characterized as having one or more “prior therapies” or as being “treatment naïve.” As used herein, unless otherwise indicated, a “prior therapy” refers to any previous systemic therapy for RCC. A “treatment naïve” subject is one that has never received any previous systemic therapy in the metastatic or adjuvant setting.

As used herein, the term “first dose” includes a single dose, but can be more than one dose, i.e., multiple doses (at least two doses, at least three doses, or more) that are administered prior to the administration of “a second dose” if the multiple doses are administered to determine the susceptibility of the patient for an anti-PD-1 antibody or anti-PD-L1 antibody therapy, i.e., differential expression of certain proteins (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, CTLA-4, TIGIT, PD-L2, or any combination thereof). The term “first dose” can also be a therapeutic dose, a dose higher than a therapeutic dose, or a subtherapeutic dose.

The term “second dose” as used herein can also include a single dose or multiple doses that are administered after the first dose (single dose or multiple doses). The second dose can be a therapeutic dose.

The use of the term “fixed dose” with regard to a composition of the invention means that two or more different antibodies in a single composition are present in the composition in particular (fixed) ratios with each other. In some embodiments, the fixed dose is based on the weight (e.g., mg) of the antibodies. In certain embodiments, the fixed dose is based on the concentration (e.g., mg/ml) of the antibodies. In some embodiments, the ratio is at least about 1:1, about 1:2, about 1:3, about 1:4, about 1:5, about 1:6, about 1:7, about 1:8, about 1:9, about 1:10, about 1:15, about 1:20, about 1:30, about 1:40, about 1:50, about 1:60, about 1:70, about 1:80, about 1:90, about 1:100, about 1:120, about 1:140, about 1:160, about 1:180, about 1:200, about 200:1, about 180:1, about 160:1, about 140:1, about 120:1, about 100:1, about 90:1, about 80:1, about 70:1, about 60:1, about 50:1, about 40:1, about 30:1, about 20:1, about 15:1, about 10:1, about 9:1, about 8:1, about 7:1, about 6:1, about 5:1, about 4:1, about 3:1, or about 2:1 mg first antibody to mg second antibody. For example, the 3:1 ratio of a first antibody and a second antibody can mean that a vial can contain about 240 mg of the first antibody and 80 mg of the second antibody or about 3 mg/ml of the first antibody and 1 mg/ml of the second antibody.

The use of the term “flat dose” with regard to the composition of the invention means a dose that is administered to a patient without regard for the weight or body surface area (BSA) of the patient. The flat dose is therefore not provided as a mg/kg dose, but rather as an absolute amount of the agent (e.g., the anti-CTLA-4 antibody and/or anti-PD-1 antibody). For example, a 60 kg person and a 100 kg person would receive the same dose of the composition (e.g., 240 mg of an anti-PD-1 antibody and 80 mg of an anti-CTLA-4 antibody in a single fixed dosing formulation vial containing both 240 mg of an anti-PD-1 antibody and 80 mg of an anti-CTLA-4 antibody (or two fixed dosing formulation vials containing 120 mg of an anti-PD-1 antibody and 40 mg of an anti-CTLA-4 antibody, etc.)).

The term “weight based dose” as referred to herein means that a dose that is administered to a patient is calculated based on the weight of the patient. For example, when a patient with 60 kg body weight requires 3 mg/kg of an anti-PD-1 antibody in combination with 1 mg/kg of an anti-CTLA-4 antibody, one can draw the appropriate amounts of the anti-PD-1 antibody (i.e., 180 mg) and the anti-CTLA-4 antibody (i.e., 60 mg) at once from a 3:1 ratio fixed dosing formulation of an anti-PD-1 antibody and an anti-CTLA-4 antibody.

“Pre-treatment” or “baseline,” as used herein, refers to the status of a subject prior to administration of a particular therapy, e.g., prior to administration of an anti-cancer agent, e.g., an immunotherapy, e.g., an anti-PD-1 antibody or an antigen binding portion thereof or an anti-PD-L1 antibody or an antigen binding portion thereof. “Pre-treatment” can refer to the status of a treatment naïve subject or to a subject who has had one or more prior therapies. Accordingly, it is possible that a subject may be considered to be “pre-treatment” even though the subject received some form of treatment or therapy at some time prior to the present treatment or therapy. Furthermore, “pre-treatment” can refer to any moment up until the moment that a treatment is administered. For example, “pre-treatment” can include weeks, days, hours, minutes, or seconds before administration of the treatment. In one particular embodiment, a “pre-treatment” sample can be collected from a subject immediately before administration of a first dose of the treatment or therapy. “Pre-treatment” and “baseline” are used interchangeably herein. As used herein, a differential expression of one or more marker genes at baseline can be determined by comparing the expression level of the one or more marker genes in a particular subject with a reference expression level of the one or more marker genes. In some embodiments, the reference expression level of the one or more marker genes is an expression level of the one or more marker genes by a non-responder to an anti-PD1 antibody or an anti-PD-L1 antibody therapy. In another embodiment, the reference expression level of the one or more marker genes is an expression level of the one or more marker genes by a subject who exhibited less than 20% tumor reduction. In other embodiments, the reference expression level of the one or more marker genes is an expression level of the one or more marker genes as measured in the average population. In other embodiments, the reference expression level of the one or more marker genes is an expression level of the one or more marker genes by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”).

“On-treatment,” as used herein, refers to the status of a subject who has received one or more initial dose of a particular therapy, e.g., an anti-cancer agent, e.g., an immunotherapy, e.g., an anti-PD-1 antibody or an antigen binding portion thereof or an anti-PD-L1 antibody or an antigen binding portion thereof. “On-treatment” can refer to a subject who has only received a single dose or a subject who has received multiple doses of the anti-PD-1 antibody or an antigen binding portion thereof or the anti-PD-L1 antibody or an antigen binding portion thereof. In some aspects, “on-treatment” refers to a subject who is receiving an ongoing regimen of a particular therapy, e.g., the subject is being treated with an anti-PD-1 antibody or an antigen binding portion thereof or an anti-PD-L1 antibody or an antigen binding portion thereof. In certain embodiments, the “on-treatment” sample can be collected from a subject on about day 1, on about day 2, on about day 3, on about day 4, on about day 5, on about day 6, on about day 7, on about day 8, on about day 9, on about day 10, on about day 11, on about day 12, on about day 13, on about day 14, on about day 15, on about day 16, on about day 17, on about day 18, on about day 19, on about day 20, on about day 21, or any combination thereof, wherein the treatment is administered on day 1. In certain embodiments, the treatment is administration of an anti-PD-1 antibody or an antigen binding portion thereof or an anti-PD-L1 antibody or an antigen binding portion thereof. In some embodiments, the anti-PD-1 antibody or an antigen binding portion thereof or the anti-PD-L1 antibody or an antigen binding portion thereof is administered on day 1 of every 21-day cycle. In certain embodiments, the on-treatment sample is collected from the subject on about day 1, on about day 2, on about day 3, on about day 4, on about day 5, on about day 6, on about day 7, on about day 8, on about day 9, on about day 10, on about day 11, on about day 12, on about day 13, on about day 14, on about day 15, on about day 16, on about day 17, on about day 18, on about day 19, on about day 20, or on about day 21 of the 21 day cycle, or any combination thereof. In one particular embodiment, the on-treatment sample is collected on day 1 of cycle 1, day 1 of cycle 2, day 8 of cycle 2, on day 1 of cycle 4, or any combination thereof. In one embodiment, the on-treatment sample is collect on day 8 of cycle 2.

Pre-treatment and on-treatment samples may be collected in the form of a tumor biopsy (e.g., a core needle biopsy), partial or complete surgical resection, blood draw, or any other method known in the art. In certain embodiments, tumor sites selected for biopsy have not received previous radiation therapy.

By way of example, an “anti-cancer agent” promotes cancer regression in a subject or prevents further tumor growth. In certain embodiments, a therapeutically effective amount of the drug promotes cancer regression to the point of eliminating the cancer. “Promoting cancer regression” means that administering an effective amount of the drug, alone or in combination with an anti-neoplastic agent, results in a reduction in tumor growth or size, necrosis of the tumor, a decrease in severity of at least one disease symptom, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction. In addition, the terms “effective,” “effectiveness,” and “efficacy” with regard to a treatment includes both pharmacological effectiveness and physiological safety. Pharmacological effectiveness refers to the ability of the drug to promote cancer regression in the patient. Physiological safety refers to the level of toxicity, or other adverse physiological effects at the cellular, organ and/or organism level (adverse effects) resulting from administration of the drug.

By way of example for the treatment of tumors, a therapeutically effective amount of an anti-cancer agent can inhibit cell growth, inhibit tumor growth, or reduce tumor size by at least about 5%, at least about 10%, by at least about 15%, at least about 20%, by at least about 25%, by at least about 30%, by at least about 40%, by at least about 50%, by at least about 60%, by at least about 70%, or by at least about 80%, by at least about 90%, by at least about 95%, or by at least about 100% relative to untreated subjects, relative to baseline, or, in certain embodiments, relative to patients treated with a standard-of-care therapy. In other embodiments of the invention, tumor regression can be observed and continue for a period of at least about 20 days, at least about 40 days, or at least about 60 days. Notwithstanding these ultimate measurements of therapeutic effectiveness, evaluation of immunotherapeutic drugs must also make allowance for “immune-related” response patterns.

An “immune-related” response pattern refers to a clinical response pattern often observed in cancer patients treated with immunotherapeutic agents that produce antitumor effects by inducing cancer-specific immune responses or by modifying native immune processes. This response pattern is characterized by a beneficial therapeutic effect that follows an initial increase in tumor burden or the appearance of new lesions, which in the evaluation of traditional chemotherapeutic agents would be classified as disease progression and would be synonymous with drug failure. Accordingly, proper evaluation of immunotherapeutic agents can require long-term monitoring of the effects of these agents on the target disease.

A therapeutically effective amount of a drug or therapeutic agent includes a “prophylactically effective amount,” which is any amount of the drug or therapeutic agent that, when administered alone or in combination with an anti-neoplastic agent to a subject at risk of developing a cancer (e.g., a subject having a pre-malignant condition) or of suffering a recurrence of cancer, inhibits the development or recurrence of the cancer. In certain embodiments, the prophylactically effective amount prevents the development or recurrence of the cancer entirely. “Inhibiting” the development or recurrence of a cancer means either lessening the likelihood of the cancer's development or recurrence, or preventing the development or recurrence of the cancer entirely.

“Differential expression,” as used herein in, refers to any expression level which is different than a reference expression level. Differential expression can refer to increased or decreased expression relative to a reference expression level. In some embodiments, differential expression can refer to the relative expression of a gene after treatment, e.g., on treatment, as compared to before treatment, e.g., at baseline. In other embodiments, differential expression can refer to the relative expression of a gene in responders as compared to non-responders.

The terms “once about every week,” “once about every two weeks,” or any other similar dosing interval terms as used herein mean approximate numbers. “Once about every week” can include every seven days ±one day, i.e., every six days to every eight days. “Once about every two weeks” can include every fourteen days ±three days, i.e., every eleven days to every seventeen days. Similar approximations apply, for example, to once about every three weeks, once about every four weeks, once about every five weeks, once about every six weeks and once about every twelve weeks. In some embodiments, a dosing interval of once about every six weeks or once about every twelve weeks means that the first dose can be administered any day in the first week, and then the next dose can be administered any day in the sixth or twelfth week, respectively. In other embodiments, a dosing interval of once about every six weeks or once about every twelve weeks means that the first dose is administered on a particular day of the first week (e.g., Monday) and then the next dose is administered on the same day of the sixth or twelfth weeks (i.e., Monday), respectively.

The use of the alternative (e.g., “or”) should be understood to mean either one, both, or any combination thereof of the alternatives. As used herein, the indefinite articles “a” or “an” should be understood to refer to “one or more” of any recited or enumerated component.

The terms “about” or “comprising essentially of” refer to a value or composition that is within an acceptable error range for the particular value or composition as determined by one of ordinary skill in the art, which will depend in part on how the value or composition is measured or determined, i.e., the limitations of the measurement system. For example, “about” or “comprising essentially of” can mean within 1 or more than 1 standard deviation per the practice in the art. Alternatively, “about” or “comprising essentially of” can mean a range of up to 10% or 20% (i.e., ±10% or ±20%). For example, about 3 mg can include any number between 2.7 mg and 3.3 mg (for 10%) or between 2.4 mg and 3.6 mg (for 20%). Furthermore, particularly with respect to biological systems or processes, the terms can mean up to an order of magnitude or up to 5-fold of a value. When particular values or compositions are provided in the application and claims, unless otherwise stated, the meaning of “about” or “comprising essentially of” should be assumed to be within an acceptable error range for that particular value or composition.

Various aspects of the invention are described in further detail in the following subsections.

II. Methods of the Invention

This disclosure provides a method of treating a subject afflicted with a tumor derived from an RCC, wherein the method comprises (i) administering to the subject a first dose of an anti-PD-1 antibody or an antigen-binding portion thereof and/or an anti PD-L1 antibody or an antigen-binding portion thereof; and (ii) administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein after the administration of the first dose, the subject exhibits an increased or decreased expression of one or more genes which is differentially regulated following treatment with an anti-PD-1 antibody, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof. The invention shows that certain genes are up- or down-regulated in a patient suffering from an RCC following initial treatment with an anti-PD-1 antibody or an antigen-binding portion thereof and/or an anti PD-L1 antibody or an antigen-binding portion thereof. Further, some genes are differentially expressed in subjects who ultimately are responsive (responders) to the treatment as compared to subjects who are not responsive (non-responders). Surprisingly, differential expression of certain genes has been found to correlate with increased patient responsiveness to anti-PD-1/anti-PD-L1 immunotherapy, e.g., reduced tumor burden. For example, as described herein, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and PD-L2 were observed to be upregulated following treatment with an anti-PD-1 antibody to a greater extent in patients who ultimately experienced a ≥20% reduction in tumor size, as compared to patient who experienced a <20% reduction in tumor size. Accordingly, certain aspects of the present invention describe methods for enhancing the treatment of patients suffering from an RCC, comprising (i) administering to a patient a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof; (ii) determining the expression of one or more differentially expressed genes (e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2); and (iii) administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti PD-L1 antibody or antigen-binding portion thereof to a patient who exhibits differential expression of the selected one or more differentially expressed genes. In some embodiments, determining includes obtaining or receiving a report from a laboratory that the patient expresses one or more differentially expressed genes (e.g., increased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2).

In some embodiments, the invention is directed to methods of (i) measuring or detecting the expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2) in a sample obtained from a subject, wherein the subject has been administered a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof; and (ii) recommending to a health care provider to administer a second dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof. The phrase “recommending a healthcare provider to administer a dose” includes, but is not limited to, sending a report that the patient who needs an anti-PD-1 antibody or anti-PD-L1 antibody therapy expresses one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2) after administration of a dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof. In another embodiment, the invention is directed to methods of (i) measuring or detecting the expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2) in a sample obtained from a subject, wherein the subject has been administered a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof; and (ii) sending a report to a health care provider to administer a second dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof.

Other embodiments are directed to methods of identifying a subject afflicted with an RCC suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy, comprising administering to the subject a first dose of an anti-PD-1 antibody or an antigen-binding portion thereof and/or an anti PD-L1 antibody or an antigen-binding portion thereof, and determining an expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) in a sample of the subject after administration of the first dose, wherein the subject exhibits differential expression of the one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) compared to the expression level prior to administration of the first dose; wherein the subject is administered a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In some embodiments, the disclosure provides a method for treating a subject afflicted with a tumor derived from an RCC comprising administering, to the subject who exhibits an differential expression of one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) after administration of a first dose of an anti-PD-1 antibody or an antigen-binding portion thereof or an anti-PD-L1 antibody or an antigen-binding portion thereof, a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof. In other embodiments, the disclosure provides a method of treating a subject afflicted with a tumor derived from an RCC, comprising: (i) determining an expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) in a sample of the subject after the subject is administered with a first dose of an anti-PD-1 antibody or an antigen-binding portion thereof or an anti-PD-L1 antibody or an antigen-binding portion thereof, wherein the subject exhibits differential expression of the one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) after the administration of the first dose and (ii) administering to the subject a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof. In certain embodiments, the disclosure provides a method of treating a subject afflicted with a tumor derived from an RCC comprising: (i) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, (ii) determining an expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) in a sample of the subject after (i), wherein the subject exhibits differential expression of the one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) compared to the expression level prior to (i); and (ii) administering to the subject a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In other embodiments, the invention is directed to a method for identifying a subject afflicted with an RCC who is suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy (“responder”) comprising determining an expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) in a sample of the subject, wherein the subject exhibits differential expression of the one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) after administration of a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof. The subject can be administered a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof. In another embodiment, the invention is directed to a method for identifying a subject afflicted with an RCC suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising: (i) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, and (ii) determining an expression level of one or more differentially expressed genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) in a sample of the subject after (i), wherein the subject exhibits differential expression of the one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) compared to the expression level prior to (i); wherein the subject is administered a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof.

In certain aspects, the invention is directed to an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof for use in treating a tumor derived from an RCC in a patient, wherein the patient has exhibited (or determined to exhibit) differential expression of one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof) after receiving a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof for use in treating a tumor derived from an RCC in a patient, wherein the patient previously received a first dose of the anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof, and wherein after receiving the first dose, the patient exhibited differential expression of one or more differentially expressed genes (e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof).

This disclosure provides a method of treating a subject afflicted with a tumor derived from an RCC, wherein the method comprises (i) administering to the subject a first dose of an anti-PD-1 antibody or an antigen-binding portion thereof and/or an anti PD-L1 antibody or an antigen-binding portion thereof; and (ii) administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein after the administration of the first dose, the subject exhibits an increased or decreased expression of one or more genes which is differentially regulated following treatment with an anti-PD-1 antibody, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof. The invention shows that certain genes are up- or down-regulated in a patient suffering from an RCC following initial treatment with an anti-PD-1 antibody or an antigen-binding portion thereof and/or an anti PD-L1 antibody or an antigen-binding portion thereof. Further, some genes are differentially expressed in subjects who ultimately are responsive (responders) to the treatment as compared to subjects who are not responsive (non-responders). Surprisingly, differential expression of certain genes has been found to correlate with increased patient responsiveness to anti-PD-1/anti-PD-L1 immunotherapy, e.g., reduced tumor burden. For example, as described herein, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and PD-L2 were observed to be upregulated following treatment with an anti-PD-1 antibody to a greater extent in patients who ultimately experienced a ≥20% reduction in tumor size, as compared to patient who experienced a <20% reduction in tumor size. Accordingly, certain aspects of the present invention describe methods for enhancing the treatment of patients suffering from an RCC, comprising (i) administering to a patient a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof; (ii) determining the expression of one or more differentially expressed genes (e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2); and (iii) administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti PD-L1 antibody or antigen-binding portion thereof to a patient who exhibits differential expression of the selected one or more differentially expressed genes. In some embodiments, determining includes obtaining or receiving a report from a laboratory that the patient expresses one or more differentially expressed genes (e.g., increased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2).

In another aspect, the invention is directed to an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof for use in treating a tumor derived from an RCC in a patient, wherein the patient exhibited (i) an increased expression of one or more serum markers of Interferon-γ activation; (ii) an increased tumor gene expression; (iii) a decreased clonality of T cell Receptor in serum; (iv) an increased T cell count in the tumor; or (v) any combination thereof after receiving a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof for use in treating a tumor derived from an RCC in a patient, wherein the patient exhibited an increased expression level of CXCL9, CXCL10, or both after receiving a first dose and/or a second dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

This disclosure further provides a method of treating a subject afflicted with a tumor derived from an RCC, wherein the method comprises (i) measuring an expression level of one or more genes selected from the group consisting of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, and (ii) administering to the subject a first dose of an antibody or an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein the subject exhibits an increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7. The invention shows that certain genes are differentially expressed at baseline in a patient suffering from an RCC as compared to the average expression level of the same genes. Further, some genes are differentially expressed in subjects who ultimately are responsive (responders) to the treatment as compared to subjects who are not responsive (non-responders). Surprisingly, differential expression of certain genes has been found to correlate with increased patient responsiveness to anti-PD-1/anti-PD-L1 immunotherapy, e.g., reduced tumor burden. For example, as described herein, MICB, PVRIG, SPI1, CLEC2B, and NKG7 were observed to be more highly expressed in patients who ultimately experienced a ≥20% reduction in tumor size, as compared to patients who experienced a <20% reduction in tumor size. Accordingly, certain aspects of the present invention describe methods for enhancing the treatment of patients suffering from an RCC, comprising (i) determining the expression of one or more differentially expressed genes (e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7) and (ii) administering to a patient a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti PD-L1 antibody or antigen-binding portion thereof to a patient who exhibits differential expression of the selected one or more differentially expressed genes. In some embodiments, determining includes obtaining or receiving a report from a laboratory that the patient expresses one or more differentially expressed genes (e.g., increased expression of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7).

In some aspects, the invention is directed to a method of identifying a subject afflicted with a tumor who is suitable for an anti-PD-1 antibody or an anti-PD-L1 antibody therapy comprising measuring an expression level of one or more genes selected from the group consisting of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject prior to the anti-PD-1 antibody or anti-PD-L1 antibody therapy. In some embodiments, the method further comprises administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to a method for identifying a subject afflicted with a tumor who is suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising measuring an expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject prior to the anti-PD-1 antibody or anti-PD-L1 antibody therapy, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”), and wherein the subject is administered a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to a method for treating a subject afflicted with a tumor comprising administering, to the subject who exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”), a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

In another aspect, the invention is directed to method for treating a subject afflicted with a tumor comprising administering a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”).

In another aspect, the invention is directed to method for treating a subject afflicted with a tumor comprising: (i) measuring an expression level of one or more genes selected from the group consisting of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, and (ii) administering to the subject a first dose of an antibody or an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof to the subject, wherein the subject exhibits an increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”).

In another aspect, the invention is directed to a method of treating a subject afflicted with a tumor comprising: (i) determining an expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”); and (ii) administering to the subject a first dose of an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof.

The expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof can be measured using any methods known in the art. In some embodiments, the expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is a protein expression measured by an immunohistochemistry, an ELISA, a western blot, a protein array or any combination thereof. In other embodiments, the expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is a nucleotide expression measured by an in situ hybridization, a DNA or RNA array or nucleotide hybridization technique, a tumor sequencing technique, a quantitative polymerase chain reaction (PCR), or any combination thereof.

In some embodiments, the expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is higher (e.g., increased) relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7 by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”). In some embodiments, the reference expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof the expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof by a non-responder to an anti-PD1 antibody or an anti-PD-L1 antibody therapy. In another embodiment, the reference expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is the expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof by a subject who exhibited less than 20% tumor reduction. In other embodiments, the reference expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is the expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof as measured in the average population. In other embodiments, the reference expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is the expression level by subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”).

In some embodiments, the expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is increased (e.g., higher), relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, by at least about 1.1 fold, at least about 1.2 fold, at least about 1.3 fold, at least about 1.4 fold, at least about 1.5 fold, at least about 1.6 fold, at least about 1.7 fold, at least about 1.8 fold, at least about 1.9 fold, at least about 2 fold, at least about 3 fold, at least about 4 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold, at least about 10 fold, at least about 15 fold, at least about 20 fold, at least about 25 fold, at least about 30 fold, at least about 35 fold, at least about 40 fold, at least about 45 fold, at least about 50 fold, at least about 60 fold, at least about 70 fold, at least about 80 fold, at least about 90 fold, or at least about 100 fold. In one particular embodiment, the expression level of MICB is increased by about 1.3 fold relative to the expression level of MICB for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”). In one particular embodiment, the expression level of PVRIG is increased by about 1.7 fold relative to the expression level of PVRIG for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”). In one particular embodiment, the expression level of NKG7 is increased by about 2 fold relative to the expression level of NKG7 for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”). In one particular embodiment, the expression level of SPI1 is increased by about 1.3 fold relative to the expression level of SPI1 for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”) for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”). In one particular embodiment, the expression level of CLEC2B is increased by about 1.9 fold relative to the expression level of CLEC2B for subjects who exhibited less than 20% tumor reduction as shown in table 6A (“No Response: Mean RMA value at baseline”).

The present methods are aimed to improve the treatment of RCCs which are among the most common tumors to show spontaneous regression (Elhilali et al. (2000) BJU Int 86:613-8; Inman et al. (2013) Eur Urol 63:881-9) while the traditional chemotherapy and radiotherapy had proven disappointing. The present methods disclosed herein increase the efficacy of anti-PD-1 and anti-PD-L1 immunotherapy by identifying a patient who is likely to respond better to an anti-PD-1 antibody or antigen binding portion thereof and/or an anti-PD-L1 antibody antigen binding portion thereof. The methods of this disclosure can be used to treat various stages of RCC, stages I, II, III, or IV. In stage I, the tumor can be 7 centimeters or smaller and is found only in the kidney. In stage II, however, the tumor can be larger than 7 centimeters and is found only in the kidney. In stage III, the tumor can be any size and cancer is found only in the kidney and in one or more nearby lymph nodes; or cancer is found in the main blood vessels of the kidney or in the layer of fatty tissue around the kidney. Cancer may also be found in one or more nearby lymph nodes. In stage IV, cancer has been spread beyond the layer of fatty tissue around the kidney and may be found in the adrenal gland above the kidney with cancer, or in nearby lymph nodes; or to other organs, such as the lungs, liver, bones, or brain, and may have spread to lymph nodes. In other embodiments, RCC that is treatable by the present methods is a recurrent RCC.

In some embodiments, the first dose is a flat dose or a weight based dose. In other embodiments, the second dose is a flat dose or a weight based dose.

Therapeutic administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof, as described herein, can effectively increase the duration of survival of the subject. In certain embodiments, therapeutic administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof to a subject results in the subject exhibiting an overall survival of at least about 10 months, at least about 11 months, at least about 12 months, at least about 13 months, at least about 14 months at least about 15 months, at least about 16 months, at least about 17 months, at least about 18 months, at least about 19 months, at least about 20 months, at least about 21 months, at least about 22 months, at least about 23 months, at least about 24 months (e.g. 2 years), at least about 25 months, at least about 26 months, at least about 27 months, at least about 28 months, at least about 29 months, at least about 30 months, at least about 31 months, at least about 32 months, at least about 33 months, at least about 34 months, at least about 35 months, at least about 3 years, at least about 4 years, at least about 5 years, at least about 6 years, at least about 7 years, at least about 8 years, at least about 9 years, at least about 10 years, or at least about 20 years after the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. The overall survival of the anti-PD-1 antibody or anti-PD-L1 antibody therapy responder is better than non-responders who are not determined to have the increased or decreased expression of the one or more biomarker genes (e.g., increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof).

In other embodiments, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof can effectively decrease the size of the tumor. Tumor size can be reduced after a first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof, after a second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof, or both. Tumor reduction can be measured by comparing the tumor size (e.g., the tumor burden) after administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof (on-treatment) to the tumor size at baseline (pre-treatment). In some embodiments, the tumor is reduced by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or about 100%. In certain embodiments, after the administration of the second dose, the tumor is reduced by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or about 100%.

In certain embodiments, the therapy of the present invention effectively increases the duration of progression free survival (PFS) of the subject. For example, the PFS of the subject can be increased by at least about 2 weeks, at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 6 months, or at least about 1 year when compared to another subject treated with only standard-of-care therapy. For example, the PFS of the subject can be increased by at least about 2 weeks, at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 6 months, or at least about 1 year when the subject exhibits an increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after the administration of a first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof, and wherein the subject is then administered a second dose, as compared to another subject treated with only standard-of-care therapy.

II. A. Differentially Expressed Genes (or Proteins Thereof)

The present disclosure provides methods of treating a subject afflicted with a tumor derived from an RCC after determining that the subject is eligible or responsive to an anti-PD-1 antibody or antigen binding portion thereof or an anti-PD-L1 antibody antigen binding portion thereof. The subject's eligibility or responsiveness can be determined by measuring or detecting (or ordering a test and receiving a report providing) the expression of the one or more differentially expressed genes (or proteins thereof). In one embodiment, a subject is eligible or responsive to an anti-PD-1 antibody or anti-PD-L1 antibody therapy if the subject shows differential expression of CTLA-4, TIGIT, PD-L2, or any combination thereof. In another embodiment, a subject is eligible or responsive to an anti-PD-1 antibody or anti-PD-L1 antibody therapy if the subject shows differential, e.g., increased, expression of MICB, PVRIG, NKG7, or any combination thereof at baseline, e.g., prior to treatment with an anti-PD-1 antibody. In another embodiment, a subject is eligible or responsive to an anti-PD-1 antibody or anti-PD-L1 antibody therapy if the subject shows differential, e.g., increased, expression of TGIT, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, or any combination thereof on treatment, e.g., after treatment with a first dose of an anti-PD-1 antibody or anti-PD-L1 antibody. In another embodiment, the subject shows differential expression of CTLA-4, TIGIT, PD-L2, CXCL9, CXCL10, and PD-L1, and any combination thereof after the administration of the first dose.

In some embodiments, the subject exhibits differential expression at baseline of MICB. In other embodiments, the subject exhibits differential expression at baseline of PVRIG. In other embodiments, the subject exhibits differential expression at baseline of NKG7. In other embodiments, the subject exhibits differential expression at baseline of SPI1. In other embodiments, the subject exhibits differential expression at baseline of CLEC2B. In some embodiments, the subject exhibits differential expression at baseline of MICB and PVRIG. In some embodiments, the subject exhibits differential expression at baseline of MICB and NKG7. In some embodiments, the subject exhibits differential expression at baseline of NKG7 and PVRIG. In some embodiments, the subject exhibits differential expression at baseline of NKG7, MICB, and PVRIG.

In some embodiments, the subject exhibits differential expression of CTLA-4 after the administration of the first dose. In other embodiments, the subject exhibits differential expression of TIGIT after the administration of the first dose. In yet other embodiments, the subject exhibits differential expression of PD-L2 after the administration of the first dose. In some embodiments, the subject exhibits differential expression of CTLA-4 and PD-L2 after the administration of the first dose. In some embodiments, the subject exhibits differential expression of CTLA-4 and TIGIT after the administration of the first dose. In some embodiments, the subject exhibits differential expression of TIGIT and PD-L2 after the administration of the first dose. In other embodiments, the subject exhibits differential expression of CTLA-4, PD-L2, and TIGIT after the administration of the first dose. In one particular embodiment, the subject exhibits differential, e.g., increased, expression of CXCL9 after the administration of the first dose. In another embodiment, the subject exhibits differential, e.g., increased, expression of CXCL10 after the administration of the first dose. In another embodiment, the subject exhibits differential expression of PD-L1 after the administration of the first dose.

In some embodiments, the subject exhibits differential, e.g., increased, expression of PVRIG after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of NKG7 after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of CD244 after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of NKTR after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of TNFSF8 after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of TNFSF13B after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of TNFRSF14 after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of SPI1 after the administration of the first dose. In some embodiments, the subject exhibits differential, e.g., increased, expression of CLEC2B after the administration of the first dose. In one embodiment, the subject exhibits differential, e.g., increased, expression of PVRIG and NKG7 after the administration of the first dose. In one particular embodiment, the subject exhibits differential, e.g., increased, expression of PVRIG and NKG7 at baseline and differentia, e.g., increased, expression of PVRIG and NKG7 after the administration of the first dose.

Other biomarker genes or proteins identified herein may be used in the present methods, either in addition to or in replacement of CTLA-4, TIGIT, and/or PD-L2. In some embodiments, the subject exhibits differential expression of one or more genes (or protein) selected from Table 2 (below) after the administration of the first dose. In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 3 (below). In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 4 (below). In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 5 (below). In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 6A and/or Table 6B (below). In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 7A and/or Table 7B (below). In other embodiments, the subject exhibits differential expression of one or more genes or proteins selected from Table 8A and or Table 8B (below).

In certain embodiments, the one or more differentially expressed genes, of which expression can be increased or decreased, include, but are not limited to, one or more genes encoding stem cell factor (SCF), vascular epithelial growth factor-3 (VEGF-3), brain-derived neurotrophic factor, vascular epithelial growth factor (VEGF), vascular epithelial growth factor-2 (VEGF-2), regulated on activation, normal T cell expressed and secreted (RANTES; chemokine (C-C motif) ligand 5 [CCL5]), vitamin D binding protein, von Willebrand factor (vWF), α-2 macroglobulin, intercellular adhesion molecule-1 (ICAM-1), monocyte chemotactic protein-1 (MCP-1; CCL2), α-1 antitrypsin, CXCL10 (IP10), vascular cell adhesion protein-1 (VCAM-1), eotaxin, tumor necrosis factor receptor-II (TNF RII), haptoglobin, tissue inhibitor of metalloproteinases-1 (TIMP-1), ferritin, IL2-RA, matrix metalloproteinase-3 (MMP-3), C reactive protein (CRP), IL-18, factor VII, β-2-microglobulin, complement 3, CXCL9 (MIG), macrophage inflammatory protein (MIP-1β; CCL4), or any combination thereof. In some embodiments, the differential expression of the one or more genes is relative to the expression of the genes prior to administration of the first dose (baseline). In one particular embodiment, the subject exhibits an increase in the expression of CXCL9, CXCL10, or both after administration of the first dose. In other embodiments, the differential expression of the one or more genes is measured by comparing the expression of the one or more genes in a responder to the expression of the one or more genes in a non-responder.

In other embodiments, the one or more differentially expressed genes, of which expression can be increased or decreased, include, but are not limited to, one or more genes selected from Table 6A, Table 7A, and Table 8A.

In addition, certain genes identified herein were observed to have higher expression levels after administration of a first dose of an anti-PD-1 antibody (on-treatment) in those subjects with a >20% reduction in tumor burden.

In addition, certain genes identified herein were observed to have lower expression levels after administration of a first dose of an anti-PD-1 antibody (on-treatment) in those subjects with a >20% reduction in tumor burden. Accordingly, these marker genes may also be used in the disclosed methods. In some embodiments, the subject exhibits a lower expression level of one or more cellular component organization genes, signaling genes, genes previously identified to be downregulated by ipilimumab in melanoma, or any combination thereof as compared to the average expression of the one or more genes in all subjects receiving the first dose.

The expression level of one or more genes identified herein at baseline (pre-treatment) can indicate a responsiveness to anti-PD-1 or an anti-PD-L1 immunotherapy. In some embodiments, prior to administration of a first dose of an anti-PD-1 antibody (baseline) the subject exhibits a lower expression level of a gene selected from NPNT, RNF152, PLLP, GALNT14, LINC00472, EPB41L1, RBPMS2, ZNF462, NFIB, SERHL, MTUS1, TDRP, TTC28, PLEKHA1, FRK, CABLES1, STON1, METTL20, TACC2, BTD, SLC24A5, UNC119B, GLCE, BTBD3, FAM117B, FAM213A, DAB2IP, RBPMS, CCDC110, DZIP3, ZNF704, DNAJC19, PTPRF, SMADS, RPL22, MBLAC1, ERMP1, TJP2, DLG3, ZNRF3, AFG3L2, RPRD2, ZHX2, IPO11∥IPO11-LRRC70, MOAP1, HSDL2, LRPPRC, SAMM50, GALK2, FGD4, C5ORF54, WWTR1, MTPAP, MRPS27, ARHGAP5, ERLIN2, MARCH6, UQCRB, FBXO3, TOMM20, LCLAT1, PEX12, GFM2, HECTD1, COQ7, LARS, LIN7C, NAPEPLD, PEX19, SCAPER, WASL, ASCC1, ZKSCAN1, MAN2A1, EIF1AX, EIF4EBP2, TTC33, AP3M2, MRPL40, MPP5, APP, THNSL1, USP53, TCAIM, ABI2, MSH3, TNFAIP1, ZNF791, SEC22A, LIPT2, PARD3, MIEF1, TBL1XR1, FBXL20, KLHL24, DCTN5, ZNF260, VAPB, CLUAP1, COX15, TMEM194B, SCAMPI, SLC25A3, ZNF12, ZMYM4, ZNF512, SERINC4, TPRG1L, and any combination thereof. In some embodiments, prior to administration of a first dose of an anti-PD-1 antibody (baseline) the subject exhibits a higher expression level of a gene selected from NANOS3, LINC01119, KCNA10, CLEC4G, TMEM105, LGALS8-AS1, ADAMTS6, RTL1, MSGN1, E2F4, SPATA31D1, FAM163B, ZSWIM1, TSPAN16, CEACAM3, C19ORF35, C11ORF24, SP9, MSLN, GALR3, TMEM190, TROAP, RP11-797H7.5, ABCB11, GDF10, KIAA1683, TMEM196, SRMS, KCNA6, C5AR2, FLJ44635, EVC, SNORA53, MUC6, SPRN, OSBP2, ZAP70, APOBEC3H, C11ORF94, MUTYH, PLEKHM2, SLC35G6, OTOS, SPRNP1, A1BG, RP11-72304.2, SYTL4, AGER, WNT5B, GFI1B, ITPRIPL1, TRAPPC1, AURKB, SLFN11, TMEM132A, KCNAB2, MYO1G, SPANXD (SPANXE), OR56A1, SIX3, SSTR4, BMP5, TMEM117, CD300E, TIMM17B, ANKRD9, ANKRD13D, ARHGEF19, CSRNP1, QRFP, TCP11, KRTAP10-3, KRTAP10-1, TMEM86B, GPR1, C11ORF88, LILRA4, TAS2R31, CIDEC, MIIP, CARD17, ZNF215, RTKN2, MYO9B, DOK1, ZNF414, TRPT1, BHLHE22, FLT3LG, RP11-290F20.1, GOLGA6L7P, SCARNA20, C2CD4C, DBNL, REG3A, LOC100288637, CDC34, ASGR2, CD7, RALGDS, CCDC22, CYTH4, C17ORF62, LINC00158, METRNL, LILRB5, IKBKE, HSH2D, KIF26B, KIFC1, MICB, SPI1, TWIST2, ROS1, LRRC29, USP15, GPR97, ELF4, MSX2, GPBAR1, CYTH1, RNF175, REG1B, CRYAA, DOK2, PPP2R2C, S100A11, LSM10, PBX4, IRS4, PTK2B, CD82, DRAP1, TCEAL5, FBXO6, SH3BP1, KCND2, DENND3, TKTL1, SAT1, IL1A, TBC1D10C, KCNN4, GBP2, FCRL3, PRAM1, EHBP1L1, FXYD5, PSTPIP1, PLEKHO1, SNORA34, SCGB1A1, PENK, CATSPER1, IL15RA, CEP128, E2F7, EGFL6, TXNDC2, VASP, HAS2, WAS, FMNL1, GADD45B, DKK2, PPAPDC1A, LTB, HIST1H3 G, ZNF101, KIAA1551, RABGAP1L, EFHD2, CTSZ, FAM20A, IGFL2, ARHGAP9, CCDC109B, IRF1, PVRIG, CTSW, CFD, BATF, MYO1F, GFPT2, TAGAP, GJB6, EVI2B, CLEC2B, SAMSN1, CLMP, PLEK, RAC2, NKG7, BIN2, SP140, CILP, IL1R2, CD3E, GBP5, GZMB, MMP3, AIM2, and any combination thereof.

The present disclosure provides that a subject can be identified as being more responsive to immunotherapy treatment with an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof by measuring the expression level of certain genes prior to administration of the immunotherapy. In some embodiments, the method of the present invention includes a method for identifying a subject afflicted with an RCC who is suitable for an anti-PD-1 antibody or anti-PD-L1 antibody therapy comprising determining the expression level of one or more genes upregulated by ipilimumab in melanoma, immune system genes (e.g., IL15RA, IL1R2, and/or IRF1), myeloid lineage genes (e.g., IL1A, LINC00158, PRAM1, and/or SPI1), lymphoid lineage genes (e.g., CD3E, AIM2, GZMB, NKG7, CD7, and/or CTSW), or any combination thereof, and administering an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof if the expression of the one or more genes is increased relative to the average expression level of the one or more genes in a select population (e.g., all RCC subjects). In other embodiments, the method comprises determining the expression level of one or more genes downregulated by ipilimumab in melanoma establishment of protein localization genes, genes coding negative regulators of epithelial cell proliferation involved in lung morphogenesis, or any combination thereof and determining that those subjects with low expression of the one or more genes relative to the average expression level of the one or more genes in a select population (e.g., all RCC subjects) may be less responsive to an anti-PD-1 or anti-PD-L1 immunotherapy.

The expression level of the one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, CTLA-4, TIGIT, and/or PD-L2, can be measured at any time, e.g., before administration of the first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof (pre-treatment); after the first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof (on-treatment); and/or after the second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof (on-treatment). In some embodiments, the baseline expression level of the one or more genes, e.g., the increased or decreased expression of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, is measured by comparing the expression of the one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, in one subject with the expression of the one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, with another subject or with the average expression of the one or more genes across a selected population of subjects (e.g., the average expression of the one or more genes by subjects affected with a tumor derived from an RCC). In some embodiments, the expression level of the one or more genes, e.g., the increased or decreased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, is measured by comparing the expression of the one or more genes, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof, prior to the administration of the first dose (pre-treatment) and after administration of the first dose (on-treatment). In other embodiments, the expression level of the one or more genes, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, is measured pre-treatment and after administration of a second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In one embodiment, the expression level of the one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, is measured at one or more time points selected from the group consisting of: pre-treatment, on about day 1, on about day 2, on about day 3, on about day 4, on about day 5, on about day 6, on about day 7, on about day 8, on about day 9, on about day 10, on about day 11, on about day 12, on about day 13, on about day 14, on about day 15, on about day 16, on about day 17, on about day 18, on about day 19, on about day 20, and on about day 21 of each 21-day cycle, wherein the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered on day 1 of each 21-day cycle. In some embodiments, the expression level of the one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, is measured during one or more 21-day cycles selected from the group consisting of: cycle 1, cycle 2, cycle 3, cycle 4, cycle 5, cycle 6, cycle 7, cycle 8, cycle 9, cycle 10, cycle 11, cycle 12, cycle 13, cycle 14, cycle 15, cycle 16, cycle 17, cycle 18, cycle 19, cycle 20, cycle 21, cycle 22, cycle 23, cycle 24, cycle 25, and after cycle 25, wherein the first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered on day 1 of cycle 1. In one particular embodiment, the expression level of MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 is measured pre-treatment and on about day 8 of cycle 2, wherein the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered on day 1 of each 21-day cycle.

Any higher or lower expression of a particular gene at baseline, as compared to the reference expression of the particular gene, can be indicative of subject's responsiveness to the anti-PD-1/anti-PD-L1 therapy. In some embodiments, a subject is considered to have increased, e.g., higher or greater, expression of one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, if the baseline expression of the one or more genes by a particular subject is at least about 1.1 fold, at least about 1.2 fold, at least about 1.3 fold, at least about 1.4 fold, at least about 1.5 fold, at least about 1.6 fold, at least about 1.7 fold, at least about 1.8 fold, at least about 1.9 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 4.5 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold, at least about 10 fold, at least about 20 fold, at least about 30 fold, at least about 40 fold, at least about 50 fold, or at least about 100 fold greater than the reference expression level of the one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7. In other embodiments, a subject is considered to have decreased, e.g., lower, expression of one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, if the baseline expression of the one or more genes by a particular subject is less than about 99%, less than about 98%, less than about 97%, less than about 96%, less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 40%, less than about 30%, less than about 20%, less than about 10%, less than about 5%, or less than about 1% that of the average expression of the one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, and/or NKG7.

Any increase or decrease in the expression of a particular gene following administration of a first dose of the anti-PD-1/anti-PD-L1 therapy can be indicative of subject's responsiveness to the anti-PD-1/anti-PD-L1 therapy. In some embodiments, a subject is considered to have increased expression of one or more genes, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, if the on-treatment expression of the one or more genes is at least about 1.1 fold, at least about 1.2 fold, at least about 1.3 fold, at least about 1.4 fold, at least about 1.5 fold, at least about 1.6 fold, at least about 1.7 fold, at least about 1.8 fold, at least about 1.9 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 4.5 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold, at least about 10 fold, at least about 20 fold, at least about 30 fold, at least about 40 fold, at least about 50 fold, or at least about 100 fold greater than the expression level of the one or more genes, e.g., PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2, at baseline (pre-treatment). In other embodiments, a subject is considered to have decreased expression of one or more genes if the on-treatment expression of the one or more genes is less than about 99%, less than about 98%, less than about 97%, less than about 96%, less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 40%, less than about 30%, less than about 20%, less than about 10%, less than about 5%, or less than about 1% that of the expression of the one or more genes at baseline (pre-treatment).

The expression of one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, or PD-L2, can be measured using any method known in the art. In some embodiments, the increase or decrease in gene expression is detected by measuring a corresponding protein expression. For example, the expression of the one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof, can be a protein expression measured by an immunohistochemistry, an ELISA, a western blot, a protein array or any combination thereof. In other embodiments, the increase or decrease in gene expression is detected by measuring corresponding messenger RNA (mRNA) levels. For example, the expression of the one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof, can be a nucleotide expression (e.g., mRNA) measured by an in situ hybridization, a DNA or RNA array or nucleotide hybridization technique, a northern blot, a tumor sequencing technique, a quantitative polymerase chain reaction (PCR), or any combination thereof.

The expression levels of the one or more genes can be measured using a sample obtained from the subject. In certain embodiments, the sample comprises tumor tissue. In some embodiments, the sample comprises the primary tumor or a metastatic lymph node. In one particular embodiment, the sample comprises a biopsy of a primary tumor or biopsy of a metastatic lymph node. In other embodiments, the sample comprises patient serum or blood.

In certain embodiments, the tumor further expresses PD-L1. The PD-L1 status of a tumor in a subject can be measured prior to administering any composition and utilizing any method disclosed herein. In some embodiments, a tumor is said to be “PD-L1 positive” if the PD-L1 expression level of a tumor (e.g., the percentage of tumor cells expressing PD-L1) is at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least about 15%, at least about 20%, or greater than 20%. In one embodiment, the PD-L1 expression level of a PD-L1 positive tumor is at least about 1%. In other embodiments, the PD-L1 expression level of a PD-L1 positive tumor is at least about 5%. In a certain embodiment, the PD-L1 expression level of a PD-L1 positive tumor is at least about 10%.

In one embodiment, a test tissue sample can be obtained from the subject who is in need of the therapy. In another embodiment, the assessment of the expression of one or more biomarker genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, PD-L1, CXCL9, and/or CXCL10, can be achieved without obtaining a test tissue sample. In some embodiments, selecting a suitable patient includes (i) optionally providing a test tissue sample obtained from a subject with cancer of the tissue, the test tissue sample comprising tumor cells and/or tumor-infiltrating inflammatory cells; and (ii) assessing the expression level of the one or more biomarker genes or the proportion of cells in the test tissue sample that express PD-L1 on the surface of the cells based on an assessment that the proportion of cells in the test tissue sample that express PD-L1 on the cell surface is higher than a predetermined threshold level.

In any of the methods comprising the measurement of gene expression in a test tissue sample as disclosed herein, however, it should be understood that any step comprising the provision of a test tissue sample obtained from a subject is an optional step. It should also be understood that in certain embodiments, the “measuring” or “assessing” step to determine the expression level of one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, CXCL9, and/or CXCL10, or to identify, or determine the number or proportion of, cells in the test tissue sample that express a gene, e.g., PD-L1, on the cell surface is performed by a transformative method of assaying for gene expression, for example by performing a reverse transcriptase-polymerase chain reaction (RT-PCR) assay or an IHC assay. In certain other embodiments, no transformative step is involved and the expression of the one or more genes is assessed by, for example, reviewing a report of test results from a laboratory. In certain embodiments, the steps of the methods up to, and including, assessing gene expression provides an intermediate result that can be provided to a physician or other healthcare provider for use in selecting a suitable candidate for the anti-PD-1 antibody or anti-PD-L1 antibody therapy. In certain embodiments, the steps that provide the intermediate result is performed by a medical practitioner or someone acting under the direction of a medical practitioner. In other embodiments, these steps are performed by an independent laboratory or by an independent person such as a laboratory technician.

In addition to the increased or decreased expression of the one or more genes, the subject can exhibit one or more additional characteristics indicative of increased responsiveness to the immunotherapy after the administration of the first dose. Those characteristics can be selected from the group consisting of: (i) an increased expression of one or more serum markers of Interferon-γ activation; (ii) an increased tumor gene expression; (iii) a decreased clonality of T cell Receptor in serum; (iv) an increased T cell count in the tumor; and (v) any combination thereof. In one particular embodiment, the one or more characteristics indicative of increased responsiveness to the immunotherapy is increased expression of one or more serum markers of Interferon-γ activation (e.g., AIM2, CASP1, CCL8, and/or IRF9). In another embodiment, the one or more characteristics indicative of increased responsiveness to the immunotherapy is increased expression of one or more tumor gene. In another embodiment, the one or more characteristics indicative of increased responsiveness to the immunotherapy is a decreased clonality of T cell Receptor in serum. In another embodiment, the one or more characteristics indicative of increased responsiveness to the immunotherapy is an increased T cell count in the tumor.

The expression level of the one or more serum markers of interferon-γ can be measured using any of the methods disclosed herein. In some embodiments, the expression of the one or more serum markers of interferon-γ, e.g., AIM2, CASP1, CCL8, and/or IRF9, is increased following administration of a first dose of an anti-PD-1 antibody, an anti-PD-L1 antibody, a fragment thereof, or any combination thereof by at least about 1.1 fold, at least about 1.2 fold, at least about 1.3 fold, at least about 1.4 fold, at least about 1.5 fold, at least about 1.6 fold, at least about 1.7 fold, at least about 1.8 fold, at least about 1.9 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 4.5 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold, at least about 10 fold, at least about 20 fold, at least about 30 fold, at least about 40 fold, at least about 50 fold, or at least about 100 fold relative to the expression level of the one or more serum markers of interferon-γ at baseline (pre-treatment).

The expression level of the tumor genes can also be measured using any of the methods disclosed herein. In some embodiments, the expression of the tumor genes is increased following administration of a first dose of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof by at least about 1.1 fold, at least about 1.2 fold, at least about 1.3 fold, at least about 1.4 fold, at least about 1.5 fold, at least about 1.6 fold, at least about 1.7 fold, at least about 1.8 fold, at least about 1.9 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 4.5 fold, at least about 5 fold, at least about 6 fold, at least about 7 fold, at least about 8 fold, at least about 9 fold, at least about 10 fold, at least about 20 fold, at least about 30 fold, at least about 40 fold, at least about 50 fold, or at least about 100 fold relative to the expression level of the tumor genes at baseline (pre-treatment).

In some embodiments, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof results in a decrease in serum (e.g., blood) T cell receptor (TCR) clonality. Subject serum T cell receptor clonality can be measured by any method known in the art, including, but not limited to, targeted next-generation sequencing of T cell receptors amplified from blood. These methods take advantage of the fact that during early T cell development, genes encoding the Ig and TCR molecules are formed by stepwise rearrangement of variable (V), diversity (D), and joining (J) gene segments, through a process referred to as V(D)J recombination (FIG. 10A). During this process, nucleotides are deleted and randomly inserted at the joining sites, yielding a diverse population of unique antigen receptors. As a result, circulating T cells can be sequenced at the Ig/TCR genes to identify the repertoire of T cell clones in a given subject, indicative of the diversity of T cells within the subject's serum. Accordingly, a high T cell clonality indicates a less diverse T cell population, and a low T cell clonality indicates a more diverse T cell population (FIG. 10A). In certain embodiments, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof results in a decrease in serum TCR clonality of at least about 2%, at least about 5%, at least about 7%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 80%, or at least about 90% relative to the serum TCR clonality at baseline. In one particular embodiment, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof results in a decrease in serum TCR clonality of at least about 50% relative to the serum TCR clonality at baseline.

In certain embodiments, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof results in an increase in tumor associated lymphocytes, e.g., T cell infiltration of the renal cancer tissue or tumor, relative to baseline, as indicated by an increase in the T cell count in the tumor. T cell infiltration can be characterized by an increased infiltration of CD4⁺ T cells, CD8⁺ T cells, or both into the renal cancer tissue or a tumor derived therefrom. This increase in T cell infiltration can be at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% greater than the level of T cell infiltration at baseline. In other embodiments, the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof results in increased T cell proliferation. T cell proliferation can be increased by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% relative to T cell proliferation at baseline. The disclosed methods can also, in certain embodiments, lead to a decrease in T-regulatory cells compared to baseline. T cell infiltration and/or proliferation and T-regulator cell counts can be measured by any method known in the art, including but not limited to, targeted next-generation sequencing of T cell receptors amplified from tumor or blood, immunohistochemistry, flow cytometry, or any combination thereof.

In other embodiments, the disclosed methods for treating RCC decreases the number of monocytic myeloid-derived suppressor cells or increases the number of granulocytic myeloid cells, relative to baseline. In one embodiment, the monocytic myeloid-derived suppressor cells are characterized by CD11b⁺/Ly6C^(hi)/Ly6G⁻ expression or CD11b⁺/Ly6C^(low)v/Ly6G⁻ expression. In another embodiment, the granulocytic myeloid cells are characterized by CD11b⁺/Ly6C⁻/Ly6G⁺ expression. The number of monocytic myeloid-derived suppressor cells can decrease by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%, relative to baseline. The number of granulocytic myeloid cells can increase by at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%, relative to baseline.

In one particular embodiment, the subject exhibits an increase in the number of CD4+ tumor associated lymphocytes in the tumor, an increase in the number of CD8+ tumor associated lymphocytes in the tumor, an increased expression level of CXCL9 in a serum, an increased expression level of CXCL10 in a serum, or any combination thereof after the administration of the first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In another embodiment, the subject exhibits an increase in the number of CD4+ tumor associated lymphocytes in the tumor, an increase in the number of CD8+ tumor associated lymphocytes in the tumor, an increased expression level of CXCL9 in a serum, an increased expression level of CXCL10 in a serum, or any combination thereof after the administration of the second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof.

II. B. Anti-PD-1 and Anti-PD-L1 Antibodies

PD-1 is a key immune checkpoint receptor expressed by activated T and B cells, which mediates immunosuppression. PD-1 is a member of the CD28 family of receptors, which includes CD28, CTLA-4, ICOS, PD-1, and BTLA. Two cell surface glycoprotein ligands for PD-1 have been identified, PD-L1 and PD-L2, which are expressed on antigen-presenting cells as well as many human cancers and have been shown to down regulate T cell activation and cytokine secretion upon binding to PD-1. Inhibition of the PD-1/PD-L1 interaction mediates potent antitumor activity in preclinical models.

Anti-PD-1 antibodies suitable for use in the disclosed methods are antibodies that bind to PD-1 with high specificity and affinity, block the binding of PD-L1, and inhibit the immunosuppressive effect of the PD-1 signaling pathway. In any of the therapeutic methods disclosed herein, an anti-PD-1 or anti-PD-L1 “antibody” includes an antigen-binding portion that binds to the PD-1 or PD-L1 receptor, respectively, and exhibits the functional properties similar to those of whole antibodies in inhibiting ligand binding and upregulating the immune system.

In other embodiments, the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof is a chimeric, humanized or, human monoclonal antibody or a portion thereof. In certain embodiments for treating a human subject, the antibody is a humanized antibody. In other embodiments for treating a human subject, the antibody is a human antibody. antibodies of an IgG1, IgG2, IgG3 or IgG4 isotype can be used.

In certain embodiments, the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof comprises a heavy chain constant region which is of a human IgG1 or IgG4 isotype. In certain other embodiments, the sequence of the IgG4 heavy chain constant region of the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof contains an S228P mutation which replaces a serine residue in the hinge region with the proline residue normally found at the corresponding position in IgG1 isotype antibodies. This mutation, which is present in nivolumab, prevents Fab arm exchange with endogenous IgG4 antibodies, while retaining the low affinity for activating Fc receptors associated with wild-type IgG4 antibodies (Wang et al. (2014) Cancer Immunol Res. 2(9):846-56). In yet other embodiments, the antibody comprises a light chain constant region which is a human kappa or lambda constant region. In other embodiments, the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof is a mAb or an antigen-binding portion thereof.

HuMAbs that bind specifically to PD-1 with high affinity have been disclosed in U.S. Pat. Nos. 8,008,449 and 8,779,105. Other anti-PD-1 mAbs have been described in, for example, U.S. Pat. Nos. 6,808,710, 7,488,802, 8,168,757 and 8,354,509, and PCT Publication No. WO 2012/145493. Each of the anti-PD-1 HuMAbs disclosed in U.S. Pat. No. 8,008,449 has been demonstrated to exhibit one or more of the following characteristics: (a) binds to human PD-1 with a K_(D) of 1×10⁻⁷ M or less, as determined by surface plasmon resonance using a Biacore biosensor system; (b) does not substantially bind to human CD28, CTLA-4 or ICOS; (c) increases T-cell proliferation in a Mixed Lymphocyte Reaction (MLR) assay; (d) increases interferon-γ production in an MLR assay; (e) increases IL-2 secretion in an MLR assay; (f) binds to human PD-1 and cynomolgus monkey PD-1; (g) inhibits the binding of PD-L1 and/or PD-L2 to PD-1; (h) stimulates antigen-specific memory responses; (i) stimulates antibody responses; and (j) inhibits tumor cell growth in vivo. Anti-PD-1 antibodies usable in the present invention include mAbs that bind specifically to human PD-1 and exhibit at least one, preferably at least five, of the preceding characteristics. In some embodiments, the anti-PD-1 antibody is nivolumab. In one embodiment, the anti-PD-1 antibody is pembrolizumab.

In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof cross-competes with nivolumab for binding to human PD-1. In one embodiment, the anti-PD-1 antibody is nivolumab. Nivolumab (also known as “OPDIVO®”; formerly designated 5C4, BMS-936558, MDX-1106, or ONO-4538) is a fully human IgG4 (S228P) PD-1 immune checkpoint inhibitor antibody that selectively prevents interaction with PD-1 ligands (PD-L1 and PD-L2), thereby blocking the down-regulation of antitumor T-cell functions (U.S. Pat. No. 8,008,449; Wang et al. (2014) Cancer Immunol Res. 2(9):846-56). In other embodiments, the anti-PD-1 antibody or fragment thereof binds to the same epitope as nivolumab. In certain embodiments, the anti-PD-1 antibody has the same CDRs as nivolumab.

In another embodiment, the anti-PD-1 antibody or fragment thereof cross-competes with pembrolizumab. In some embodiments, the anti-PD-1 antibody or fragment thereof binds to the same epitope as pembrolizumab. In certain embodiments, the anti-PD-1 antibody has the same CDRs as pembrolizumab. In another embodiment, the anti-PD-1 antibody is pembrolizumab. Pembrolizumab (also known as “KEYTRUDA®,” lambrolizumab, and MK-3475) is a humanized monoclonal IgG4 antibody directed against human cell surface receptor PD-1 (programmed death-1 or programmed cell death-1). Pembrolizumab is described, for example, in U.S. Pat. Nos. 8,354,509 and 8,900,587; see also http://www.cancer.gov/drugdictionary?cdrid=695789 (last accessed: Dec. 14, 2014). Pembrolizumab has been approved by the FDA for the treatment of relapsed or refractory melanoma.

In other embodiments, the anti-PD-1 antibody or fragment thereof cross-competes with MEDI0608. In still other embodiments, the anti-PD-1 antibody or fragment thereof binds to the same epitope as MEDI0608. In certain embodiments, the anti-PD-1 antibody has the same CDRs as MEDI0608. In some embodiments, the anti-PD-1 antibody is MEDI0608 (formerly AMP-514), which is a monoclonal antibody. MEDI0608 is described, for example, in U.S. Pat. No. 8,609,089B2 or in http://www.cancer.gov/drugdictionary?cdrid=756047 (last accessed Dec. 14, 2014).

In certain embodiments, an immune checkpoint inhibitor is AMP-224, which is a B7-DC Fc fusion protein. AMP-224 is discussed in U.S. Publ. No. 2013/0017199 or in http://www.cancer.gov/publications/dictionaries/cancer-drug?cdrid=700595 (last accessed Jul. 8, 2015).

In other embodiments, the anti-PD-1 antibody or fragment thereof cross-competes with BGB-A317. In some embodiments, the anti-PD-1 antibody or fragment thereof binds the same epitope as BGB-A317. In certain embodiments, the anti-PD-1 antibody has the same CDRs as BGB-A317. In certain embodiments, the anti-PD-1 antibody is BGB-A317, which is a humanized monoclonal antibody. BGB-A317 is described in U.S. Publ. No. 2015/0079109.

Anti-PD-1 antibodies usable in the disclosed methods also include isolated antibodies that bind specifically to human PD-1 and cross-compete for binding to human PD-1 with nivolumab (see, e.g., U.S. Pat. Nos. 8,008,449 and 8,779,105; WO 2013/173223). The ability of antibodies to cross-compete for binding to an antigen indicates that these antibodies bind to the same epitope region of the antigen and sterically hinder the binding of other cross-competing antibodies to that particular epitope region. These cross-competing antibodies are expected to have functional properties very similar those of nivolumab by virtue of their binding to the same epitope region of PD-1. Cross-competing antibodies can be readily identified based on their ability to cross-compete with nivolumab in standard PD-1 binding assays such as Biacore analysis, ELISA assays or flow cytometry (see, e.g., WO 2013/173223).

In certain embodiments, the antibodies that cross-compete for binding to human PD-1 with, or bind to the same epitope region of human PD-1 as, nivolumab are mAbs. For administration to human subjects, these cross-competing antibodies are preferably chimeric antibodies, or more preferably humanized or human antibodies. Such chimeric, humanized or human mAbs can be prepared and isolated by methods well known in the art.

Anti-PD-1 antibodies usable in the methods of the disclosed invention also include antigen-binding portions of the above antibodies. It has been amply demonstrated that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Examples of binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the V_(L), V_(H), C_(L) and C_(H1) domains; (ii) a F(ab′)₂ fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the V_(H) and C_(H1) domains; and (iv) a Fv fragment consisting of the V_(L) and V_(H) domains of a single arm of an antibody.

Anti-PD-1 antibodies suitable for use in the disclosed compositions are antibodies that bind to PD-1 with high specificity and affinity, block the binding of PD-L1 and or PD-L2, and inhibit the immunosuppressive effect of the PD-1 signaling pathway. In any of the compositions or methods disclosed herein, an anti-PD-1 “antibody” includes an antigen-binding portion or fragment that binds to the PD-1 receptor and exhibits the functional properties similar to those of whole antibodies in inhibiting ligand binding and upregulating the immune system. In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof cross-competes with nivolumab for binding to human PD-1. In other embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is a chimeric, humanized or human monoclonal antibody or a portion thereof. In certain embodiments, the antibody is a humanized antibody. In other embodiments, the antibody is a human antibody. Antibodies of an IgG1, IgG2, IgG3 or IgG4 isotype can be used.

In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof comprises a heavy chain constant region which is of a human IgG1 or IgG4 isotype. In certain other embodiments, the sequence of the IgG4 heavy chain constant region of the anti-PD-1 antibody or antigen-binding portion thereof contains an S228P mutation which replaces a serine residue in the hinge region with the proline residue normally found at the corresponding position in IgG1 isotype antibodies. This mutation, which is present in nivolumab, prevents Fab arm exchange with endogenous IgG4 antibodies, while retaining the low affinity for activating Fc receptors associated with wild-type IgG4 antibodies (Wang et al. (2014)). In yet other embodiments, the antibody comprises a light chain constant region which is a human kappa or lambda constant region. In other embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is a mAb or an antigen-binding portion thereof.

In certain embodiments of any of the therapeutic methods described herein comprising administration of an anti-PD-1 antibody, the anti-PD-1 antibody is nivolumab. In other embodiments, the anti-PD-1 antibody is pembrolizumab. In other embodiments, the anti-PD-1 antibody is chosen from the human antibodies 17D8, 2D3, 4H1, 4A11, 7D3 and 5F4 described in U.S. Pat. No. 8,008,449. In still other embodiments, the anti-PD-1 antibody is MEDI0608 (formerly AMP-514), AMP-224, or BGB-A317.

Anti-PD-1 antibodies usable in the methods of the disclosed invention also include antigen-binding portions of the above antibodies. It has been amply demonstrated that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Examples of binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the V_(L), V_(H), C_(L) and C_(H1) domains; (ii) a F(ab′)₂ fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the V_(H) and C_(H1) domains; and (iv) a Fv fragment consisting of the V_(L) and V_(H) domains of a single arm of an antibody.

In certain embodiments, an anti-PD-1 antibody used in the methods can be replaced with another PD-1 or anti-PD-L1 antagonist. For example, because an anti-PD-L1 antibody prevents interaction between PD-1 and PD-L1, thereby exerting similar effects to the signaling pathway of PD-1, an anti-PD-L1 antibody can replace the use of an anti-PD-1 antibody in the methods disclosed herein. Therefore, in one embodiment, the present invention is directed to a method for treating a subject afflicted with a non-squamous NSCLC comprising administering to the subject a therapeutically effective amount an anti-PD-L1 antibody.

In certain embodiments, the anti-PD-L1 antibody is BMS-936559 (formerly 12A4 or MDX-1105) (see, e.g., U.S. Pat. No. 7,943,743; WO 2013/173223).

In other embodiments, the anti-PD-L1 antibody is MPDL3280A (also known as RG7446) (see, e.g., Herbst et al. (2013) J Clin Oncol 31(suppl):3000. Abstract.; U.S. Pat. No. 8,217,149).

In other embodiments, the anti-PD-L1 antibody is MEDI4736 (also called Durvalumab; Khleif (2013) In: Proceedings from the European Cancer Congress 2013; Sep. 27-Oct. 1, 2013; Amsterdam, The Netherlands. Abstract 802, See U.S. Pat. No. 8,779,108 or US 2014/0356353, filed May 6, 2014).

In further embodiments, the anti-PD-L1 antibody is MSB0010718C (also called Avelumab; See US 2014/0341917).

Because anti-PD-1 and anti-PD-L1 target the same signaling pathway and have been shown in clinical trials to exhibit similar levels of efficacy in a variety of cancers, including RCC (see Brahmer et al. (2012) N Engl J Med 366:2455-65; Topalian et al. (2012a) N Engl J Med 366:2443-54; WO 2013/173223), an anti-PD-L1 antibody can be substituted for the anti-PD-1 antibody in any of the therapeutic methods disclosed herein. In certain embodiments, the anti-PD-L1 antibody is BMS-936559 (formerly 12A4 or MDX-1105) (see, e.g., U.S. Pat. No. 7,943,743; WO 2013/173223). In other embodiments, the anti-PD-L1 antibody is MPDL3280A (also known as RG7446) (see, e.g., Herbst et al. (2013) J Clin Oncol 31(suppl):3000. Abstract; U.S. Pat. No. 8,217,149) or MEDI4736 (Khleif (2013) In: Proceedings from the European Cancer Congress 2013; Sep. 27-Oct. 1, 2013; Amsterdam, The Netherlands. Abstract 802). In certain embodiments, the antibodies that cross-compete for binding to human PD-L1 with, or bind to the same epitope region of human PD-L1 as the above-references PD-L1 antibodies are mAbs. For administration to human subjects, these cross-competing antibodies can be chimeric antibodies, or can be humanized or human antibodies. Such chimeric, humanized or human mAbs can be prepared and isolated by methods well known in the art.

In some embodiments, an immune checkpoint inhibitor, e.g., an anti-PD-1 antagonist, used in the present invention is a PD-1 Fc fusion protein.

The anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof of the present invention can be administered to a subject at a dose (either a first dose or a second dose) selected from the group consisting of about 0.1 mg/kg, about 0.2 mg/kg, about 0.3 mg/kg, about 0.4 mg/kg, about 0.5 mg/kg, about 0.6 mg/kg, about 0.7 mg/kg, about 0.8 mg/kg, about 0.9 mg/kg, about 1.0 mg/kg, about 1.1 mg/kg, about 1.2 mg/kg, about 1.3 mg/kg, about 1.4 mg/kg, about 1.5 mg/kg, about 2.0 mg/kg, about 2.5 mg/kg, about 3.0 mg/kg, about 3.5 mg/kg, about 4.0 mg/kg, about 4.5 mg/kg, about 5.5 mg/kg, about 6.5 mg/kg, about 7.5 mg/kg, about 8.0 mg/kg, about 8.5 mg/kg, about 9.0 mg/kg, about 9.5 mg/kg, about 10 mg/kg, about 11 mg/kg, about 12 mg/kg, about 13 mg/kg, about 14 mg/kg, about 15 mg/kg, about 20 mg/kg, or greater than about 20 mg/kg. In other embodiments, the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof, can be administered at a dose selected from the group consisting of about 0.1 to about 20.0 mg/kg, about 0.1 to about 15.0 mg/kg, about 0.1 to about 10.0 mg/kg, about 0.1 to about 9.5 mg/kg, about 0.1 to about 9.0 mg/kg, about 0.1 to about 8.5 mg/kg, about 0.1 to about 8.0 mg/kg, about 0.1 to about 7.5 mg/kg, about 0.1 to about 7.0 mg/kg, about 0.1 to about 6.5 mg/kg, about 0.1 to about 6.0 mg/kg, about 0.1 to about 5.5 mg/kg, about 0.1 to about 5.0 mg/kg, about 0.1 to about 4.5 mg/kg, about 0.1 to about 4.0 mg/kg, about 0.1 to about 3.5 mg/kg, about 0.1 to about 3.0 mg/kg, about 0.3 to about 10.0 mg/kg, about 0.3 to about 9.0 mg/kg, about 0.3 to about 6.0 mg/kg, about 0.3 to about 3.0 mg/kg, about 3.0 to about 10.0 mg/kg, about 3.0 to about 9.0 mg/kg, or about 3.0 to about 6.0 mg/kg. In certain embodiments, a subject is administered 0.3 mg/kg of an anti-PD-1 antibody, e.g., nivolumab, or an anti-PD-L1 antibody. In other embodiments, a subject is administered 2.0 mg/kg of an anti-PD-1 antibody, e.g., nivolumab, or an anti-PD-L1 antibody. In other embodiments, a subject is administered 10 mg/kg of an anti-PD-1 antibody, e.g., nivolumab, or an anti-PD-L1 antibody.

II. C. Combination Therapies with Anti-PD-1 and/or Anti-PD-L1 Antibodies

In some embodiments, the methods disclosed herein further comprise administering one or more additional anti-cancer agents. In certain embodiments, the one or more anti-cancer agents have been administered to the subject prior to the administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In certain embodiments, the one or more anti-cancer agents were not effective in treating the cancer. In some embodiments, the other anti-cancer agent is any anti-cancer agent described herein or known in the art. In certain embodiments, the anti-PD-1 antibody or anti-PD-L1 antibody can be combined with another immunotherapy. In certain embodiments, immunotherapy involving blockade of immune checkpoints is administered as a monotherapy. In other embodiments, immunotherapy involving blockade of immune checkpoints is administered in combination with other therapies.

When the anti-PD-1 antibody or anti-PD-L1 antibody is combined with another anti-cancer agent, the anti-PD-1 antibody or anti-PD-L1 antibody and the second anti-cancer agent can be administered at a fixed dose. In some embodiments, the dosage of the anti-PD-1 antibody or anti-PD-L1 antibody and the second anti-cancer agent can be flat doses or fixed doses.

In some embodiments, the anti-cancer agent is selected from the group consisting of an antibody or antigen-binding portion thereof that binds specifically to CTLA-4 (“anti-CTLA-4 antibody or antigen-binding portion thereof”) and inhibits CTLA-4 activity, a chemotherapy, a platinum-based doublet chemotherapy, a TKI, an anti-VEGF inhibitor, or any combination thereof. In one embodiment, the other anti-cancer agent is an anti-CTLA antibody. In another embodiment, the other anti-cancer agent is a chemotherapy or a platinum-based doublet chemotherapy (PT-DC). In certain embodiments, the other anti-cancer agent is an EGFR-targeted TKI. In one embodiment, the other anti-cancer agent is an anti-VEGF antibody. In other embodiments, the anti-cancer agent is a platinum agent (e.g., cisplatin, carboplatin), a mitotic inhibitor (e.g., paclitaxel, albumin-bound paclitaxel, docetaxel, taxotere, docecad), a fluorinated Vinca alkaloid (e.g., vinflunine, javlor), vinorelbine, vinblastine, etoposide, or pemetrexed gemcitabin. In one embodiment, the other anti-cancer agent is 5-flurouracil (5-FU). In certain embodiments, the other anti-cancer agent is any other anti-cancer agent known in the art. In some embodiments, two or more additional anti-cancer agents are administered in combination with the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In some embodiments, administration of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is combined with surgical resection, radiation therapy, and or any other standard-of-care treatment of RCC known in the art.

1. Anti-CTLA-4 Antibodies

In certain embodiments, an anti-PD-1 antibody or anti-PD-L1 antibody is combined with an anti-CTLA-4 antibody. CTLA-4 interaction with B7 transduces a signal leading to inactivation of T-cells bearing the CTLA-4 receptor. Disruption of this interaction effectively induces, enhances, or prolongs the activation of such T cells, thereby inducing, enhancing, or prolonging an immune response. Previous studies have found that RCC patients treated with a combination of an anti-PD-1 antibody (e.g., nivolumab) and an anti-CTLA-4 antibody (e.g., ipilimumab) exhibit increased objective response rates (ORRs) relative to treatment with nivolumab alone. See International Application No. PCT/US2015/018727, which is incorporated by reference herein in its entirety. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered to a subject in combination with an anti-cancer agent, wherein the anti-cancer agent is an antibody or antigen-binding portion thereof that binds specifically to CTLA-4 and inhibits CTLA-4 activity. In one particular embodiment, the anti-cancer agent is ipilimumab.

HuMAbs that bind specifically to CTLA-4 with high affinity have been disclosed in U.S. Pat. Nos. 6,984,720 and 7,605,238. Other anti-CTLA-4 mAbs have been described in, for example, U.S. Pat. Nos. 5,977,318, 6,051,227, 6,682,736, and 7,034,121. The anti-CTLA-4 HuMAbs disclosed in U.S. Pat. Nos. 6,984,720 and 7,605,238 have been demonstrated to exhibit one or more of the following characteristics: (a) binds specifically to human CTLA-4 with a binding affinity reflected by an equilibrium association constant (K_(a)) of at least about 10⁷ M⁻¹, or about 10⁹ M⁻¹, or about 10¹⁰ M⁻¹ to 10¹¹ M⁻¹ or higher, as determined by Biacore analysis; (b) a kinetic association constant (k_(a)) of at least about 10³, about 10⁴, or about 10⁵ m⁻¹ s⁻¹; (c) a kinetic disassociation constant (k_(d)) of at least about 10³, about 10⁴, or about 10⁵ m⁻¹ s⁻¹; and (d) inhibits the binding of CTLA-4 to B7-1 (CD80) and B7-2 (CD86). Anti-CTLA-4 antibodies usable in the present method include mAbs that bind specifically to human CTLA-4 and exhibit at least one, at least two or, in one embodiment, at least three of the preceding characteristics.

An exemplary clinical anti-CTLA-4 antibody useful for the combination is the human mAb 10D1 (now known as ipilimumab and marketed as YERVOY®) as disclosed in U.S. Pat. No. 6,984,720. Ipilimumab is an anti-CTLA-4 antibody that can be used in the methods disclosed herein. Ipilimumab is a fully human, IgG1 monoclonal antibody that blocks the binding of CTLA-4 to its B7 ligands, thereby stimulating T cell activation and improving overall survival (OS) in patients with advanced melanoma (Hodi et al. (2010) N Engl J Med 363:711-23). Concurrent therapy with nivolumab and ipilimumab in a Phase 1 clinical trial produced rapid and deep tumor regression in a substantial proportion of patients with advanced melanoma, and was significantly more effective than either antibody alone (Wolchok et al. (2013) N Engl J Med 369(2):122-33; WO 2013/173223).

Another anti-CTLA-4 antibody usable in the present methods is tremelimumab (also known as CP-675,206). Tremelimumab is human IgG2 monoclonal anti-CTLA-4 antibody. Tremelimumab is described in WO/2012/122444, U.S. Publ. No. 2012/263677, or WO Publ. No. 2007/113648 A2.

Anti-CTLA-4 antibodies usable in the disclosed methods also include isolated antibodies that bind specifically to human CTLA-4 and cross-compete for binding to human CTLA-4 with ipilimumab or tremelimumab or bind to the same epitope region of human CTLA-4 as ipilimumab or tremelimumab. In certain embodiments, the antibodies that cross-compete for binding to human CTLA-4 with, or bind to the same epitope region of human CTLA-4 as does ipilimumab or tremelimumab, are antibodies comprising a heavy chain of the human IgG1 isotype. For administration to human subjects, these cross-competing antibodies are preferably chimeric antibodies, or more preferably humanized or human antibodies. Usable anti-CTLA-4 antibodies also include antigen-binding portions of the above antibodies such as Fab, F(ab′)₂, Fd or Fv fragments.

In some embodiments, the method of the present invention further comprises administering an anti-CTLA-4 antibody or antigen-binding portion thereof to the subject. The anti-CTLA-4 antibody or antigen-binding portion thereof can be administered before, after, or concurrently with the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof, or any combination thereof. In some embodiments, the anti-CTLA-4 antibody or antigen-binding portion thereof is administered before the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In other embodiments, the anti-CTLA-4 antibody or antigen-binding portion thereof is administered after the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In other embodiments, the anti-CTLA-4 antibody or antigen-binding portion thereof is administered at the same time as the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof.

2. Combinations with Other Standard-of-Care Treatments

In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with any other known standard-of-care treatment of RCC. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with one or more of surgical resection, including radical nephrectomy, partial nephrectomy, cytoreductive nephrectomy, and nephron-sparing surgery; radiotherapy; chemotherapy; treatment with cytokines IL-2 and IFNα, e.g., IFN-2b and PegIFN-2b; mTOR inhibitors, e.g., everolimus and temsirolimus; or any combination thereof.

Standard-of-care therapies for different types of cancer are well known by persons of skill in the art. For example, the National Comprehensive Cancer Network (NCCN), an alliance of 21 major cancer centers in the USA, publishes the NCCN Clinical Practice Guidelines in Oncology (NCCN GUIDELINES®) that provide detailed up-to-date information on the standard-of-care treatments for a wide variety of cancers (see NCCN GUIDELINES®, 2014).

For clinically localized RCC (Stage IA and IB), surgical resection, including radical nephrectomy and nephron-sparing surgery, is an effective therapy. Partial nephrectomy is generally not suitable for patients with locally advanced tumors (Stage II and III), in which case radical nephrectomy is preferred. Where the tumor is confined to the renal parenchyma, the 5-year survival rate is 60-70%, but this is lowered considerably in Stage IV disease where metastases have spread. Stage IV RCC is relatively resistant to radiotherapy and chemotherapy, although patients can benefit from surgery, and cytoreductive nephrectomy before systemic therapy is recommended for patients with a potentially surgically resectable primary and multiple resectable metastases.

In some embodiments, the standard of care that can be combined with the anti-PD-1 or anti-PD-L1 therapy includes IL-2 and interferon (IFN) a, e.g., IFN-2b and PegIFN-2b.

The recognition of the importance of hypoxia inducible factor alpha (HIFα) signaling in the pathogenesis of clear-cell RCC has led to widespread study of two classes of targeted therapies, anti-angiogenic TKIs and mTOR inhibitors, in 1L and 2L treatments (Mulders (2009) BJU Int 104:1585-89). Targeting of angiogenesis is rational because constitutive HIFα activation leads to the upregulation or activation of several proteins including vascular endothelial growth factor (VEGF), which can subsequently lead to tumor proliferation and neovasculature formation. Moreover, blockade of VEGF activity may modulate the immune environment and stimulate an antitumor response. Targeting of the mTOR pathway is important because activation of the upstream PI3K/Akt/mTOR signaling pathway is one method by which constitutive HIFα activation or upregulation occurs (Mulders (2009) BJU Int 104:1585-89).

Agents that target angiogenesis include VEGF-receptor (VEGFr) TKIs (e.g., sorafenib, sunitinib, pazopanib, axitinib, and tivozanib) and VEGF-binding mAbs (e.g., bevacizumab), while agents that target the mTOR pathway include the mTOR inhibitors (e.g., everolimus and temsirolimus) (Mulders (2009) BJU Int 104:1585-89; NCCN GUIDELINES®, Version 3.2014—Kidney Cancer). However, durable responses are rare as most patients develop resistance and eventually progressive disease, and OS improvement has only been shown in one phase 3 trial in poor-risk patients: temsirolimus (TORISEL®) showed a statistically significant benefit for OS in patients with advanced RCC compared to IFNα (10.9 months versus 7.3 months) (Hudes et al. (2007) N Engl J Med 356(22):2271-81). Everolimus (AFINITOR®) has also demonstrated a 2.1-month improvement in median progression-free survival (PFS) versus placebo, but with no OS improvement (Motzer et al. (2008) Lancet 372:449-56). Among the five approved anti-angiogenic agents (sorafenib, sunitinib, pazopanib, axitinib, and bevacizumab) and two approved mTOR inhibitors (temsirolimus, everolimus), only everolimus is approved specifically for use after the failure of treatment with anti-angiogenic therapy. In the U.S., everolimus is indicated for the treatment of advanced RCC after failure of first-line treatment with sunitinib or sorafenib, whereas in the EU, everolimus is more broadly indicated for patients with advanced RCC, whose disease has progressed on or after treatment with VEGF-targeted therapy. No recommendation exists for patients progressing on mTOR inhibitors.

In certain embodiments, the anti-PD-1 antibody or antigen binding portion thereof or the anti-PD-L1 antibody antigen binding portion thereof can be administered to a subject suffering from a renal cancer in addition to (e.g., co-administered), prior to, or following a standard-of-care therapy, or any combination thereof. In some embodiments, the antibodies of the present invention can be administered before the subject is administered one or more standard-of-care therapies. In other embodiments, the antibodies of the present invention can be administered after the subject has received one or more standard-of-care therapies. In other embodiments, the antibodies of the present invention can be administered at the same time (e.g., concurrently or as part of the same course of treatment) as one or more standard-of-care therapies. In certain embodiments, a subject is administered an anti-PD-1 antibody or antigen binding portion thereof or an anti-PD-L1 antibody antigen binding portion thereof and an anti-angiogenic TKI. In one particular embodiment, the TKI is selected from sunitinib, pazopanib, sorafenib, axitinib, or tivozanib.

Vascular endothelial growth factor (“VEGF”) is an endothelial cell-specific mitogen and an inducer of angiogenesis. VEGF has a prominent role in angiogenesis and tumor growth and development. In some embodiments of this invention, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with an anti-VEGF antagonist. In certain embodiments, the anti-VEGF antagonist is an anti-VEGF antibody or an antigen-binding molecule or fragment thereof. In certain embodiments, the anti-VEGF antibody is bevacizumab (described in U.S. Pat. No. 7,169,901), or any other VEGF antibody known in the art including ranibizumab (U.S. Pat. No. 7,297,334), VGX-100 (U.S. Pat. No. 7,423,125), r84 (U.S. Pat. No. 8,034,905), aflibercept (U.S. Pat. No. 5,952,199), IMC-18F1 (U.S. Pat. No. 7,972,596), IMC-1C11 (PCT/US2000/02180), and ramucirumab (U.S. Pat. No. 7,498,414).

In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with any chemotherapy known in the art. In certain embodiments, the chemotherapy is a platinum based-chemotherapy. Platinum-based chemotherapies are coordination complexes of platinum. In some embodiments, the platinum-based chemotherapy is a platinum-doublet chemotherapy. In one embodiment, the chemotherapy is administered at the approved dose for the particular indication. In other embodiments, the chemotherapy is administered at any dose disclosed herein. In some embodiments, the platinum-based chemotherapy is cisplatin, carboplatin, oxaliplatin, satraplatin, picoplatin, Nedaplatin, Triplatin, Lipoplatin, or combinations thereof. In certain embodiments, the platinum-based chemotherapy is any other platinum-based chemotherapy known in the art. In some embodiments, the chemotherapy is the nucleotide analog gemcitabine. In an embodiment, the chemotherapy is a folate antimetabolite. In an embodiment, the folate antimetabolite is pemetrexed. In certain embodiments the chemotherapy is a taxane. In other embodiments, the taxane is paclitaxel. In other embodiments, the chemotherapy is a nucleoside analog. In one embodiment, the nucleoside analog is gemcitabine. In some embodiments, the chemotherapy is any other chemotherapy known in the art. In certain embodiments, at least one, at least two or more chemotherapeutic agents are administered in combination with the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with gemcitabine and cisplatin. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with pemetrexed and cisplatin. In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with gemcitabine and pemetrexed. In one embodiment, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with paclitaxel and carboplatin. In an embodiment, an anti-CTLA-4 antibody is additionally administered.

In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof are administered in combination with a TKI. In certain embodiments, the tyrosine kinase inhibitor is pazopanib, sorafenib, sunitinib, axitinib, tivozanib, gefitinib, erlotinib, any combination thereof, or any other tyrosine kinase inhibitor known in the art. In some embodiments, the tyrosine kinase inhibitor act on the epidermal growth factor receptor (EGFR). In an embodiment, an anti-CTLA-4 antibody is additionally administered.

III. Pharmaceutical Compositions and Dosages

Therapeutic agents of the present invention can be constituted in a composition, e.g., a pharmaceutical composition containing an antibody or antigen-binding portion thereof and a pharmaceutically acceptable carrier. As used herein, a “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. In one embodiment, the carrier for a composition containing an antibody is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion), whereas the carrier for a composition containing a TKI is suitable for non-parenteral, e.g., oral, administration. In one particular embodiment, the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof is formulated for intravenous administration. A pharmaceutical composition of the invention can include one or more pharmaceutically acceptable salts, anti-oxidant, aqueous and non-aqueous carriers, and/or adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents.

Dosage regimens are adjusted to provide the optimum desired response, e.g., a maximal therapeutic response and/or minimal adverse effects. For administration of an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof, as a monotherapy or in combination with another anti-cancer agent, the dosage can range from about 0.01 to about 20 mg/kg, about 0.1 to about 10 mg/kg, about 0.1 to about 5 mg/kg, about 1 to about 5 mg/kg, about 2 to about 5 mg/kg, about 7.5 to about 12.5 mg/kg, or about 0.1 to about 30 mg/kg of the subject's body weight. For example, dosages can be about 0.1, about 0.3, about 1, about 2, about 3, about 5, or about 10 mg/kg body weight, or about 0.3, about 1, about 2, about 3, or about 5 mg/kg body weight. In one particular embodiment, the first dose is administered at a dose ranging from at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight. In another embodiment, the second dose is administered at a dose ranging from at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight.

In some embodiments, the dosage of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof comprises a dose ranging from at least about 10 mg to at least about 1200 mg, at least about 10 mg to at least about 1100 mg, at least about 10 mg to at least about 1000 mg, at least about 10 mg to at least about 900 mg, at least about 10 mg to at least about 800 mg, at least about 10 mg to at least about 700 mg, at least about 10 mg to at least about 600 mg, at least about 10 mg to at least about 500 mg, at least about 10 mg to at least about 400 mg, at least about 10 mg to at least about 300 mg, at least about 10 mg to at least about 200 mg, at least about 10 mg to at least about 100 mg, at least about 20 mg to at least about 1200 mg, at least about 30 mg to at least about 1100 mg, at least about 40 mg to at least about 1000 mg, at least about 50 mg to at least about 900 mg, at least about 60 mg to at least about 800 mg, at least about 70 mg to at least about 800 mg, at least about 80 mg to at least about 800 mg, at least about 90 mg to at least about 800 mg, at least about 100 mg to at least about 1000 mg, at least about 100 mg to at least about 900 mg, at least about 100 mg to at least about 800 mg, at least about 100 mg to at least about 700 mg, at least about 100 mg to at least about 600 mg, or at least about 100 mg to at least about 500 mg. In one particular embodiment, the first dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg. In another embodiment, the second dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg.

In some embodiments, the first dose and/or the second dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof comprises a dose of at least about 10 mg, at least about 20 mg, at least about 30 mg, at least about 40 mg, at least about 50 mg, at least about 60 mg, at least about 70 mg, at least about 80 mg, at least about 90 mg, at least about 100 mg, at least about 110 mg, at least about 120 mg, at least about 130 mg, at least about 140 mg, at least about 150 mg, at least about 160 mg, at least about 170 mg, at least about 180 mg, at least about 190 mg, at least about 200 mg, at least about 220 mg, at least about 240 mg, at least about 260 mg, at least about 280 mg, at least about 300 mg, at least about 350 mg, at least about 400 mg, at least about 450 mg, at least about 500 mg, at least about 550 mg, at least about 600 mg, at least about 650 mg, at least about 700 mg, at least about 800 mg, at least about 900 mg, at least about 1000 mg, or at least about 1500 mg.

In some embodiments, the first dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg or at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight. In other embodiments, the second dose is administered at a dose ranging from at least about 80 mg to at least about 800 mg or at least about 0.1 mg/kg to at least about 10.0 mg/kg body weight.

The dosing schedule is typically designed to achieve exposures that result in sustained receptor occupancy (RO) based on typical pharmacokinetic properties of an antibody. An exemplary treatment regime entails administration about once per week, once about every 2 weeks, once about every 3 weeks, once about every 4 weeks, once about a month, once about every 3-6 months or longer. In certain embodiments, an anti-PD-1 antibody or antigen-binding portion thereof and/or an anti-PD-L1 antibody or antigen-binding portion thereof is administered to the subject once about every 2 weeks. In other embodiments, the antibody or antigen-binding portion thereof is administered once about every 3 weeks. The dosage and scheduling can change during a course of treatment. For example, a dosing schedule for anti-PD-1 or anti-PD-L1 monotherapy can comprise administering the Ab: (i) about every 2 weeks in about 6-week cycles; (ii) about every 4 weeks for about six dosages, then about every three months; (iii) about every 3 weeks; (iv) about 3 to about 10 mg/kg once followed by about 1 mg/kg every about 2-3 weeks. Considering that an IgG4 antibody typically has a half-life of 2-3 weeks, a dosage regimen for an anti-PD-1 antibody or an anti-PD-L1 antibody of the invention comprises at least about 0.3 to at least about 10 mg/kg body weight, at least about 1 to at least about 5 mg/kg body weight, or at least about 1 to at least about 3 mg/kg body weight via intravenous administration, with the antibody being given every about 14-21 days in up to about 6-week or about 12-week cycles until complete response or confirmed progressive disease. In certain embodiments, an anti-PD-1 or an anti-PD-L1 monotherapy is administered at 3 mg/kg every 2 weeks until progressive disease or unacceptable toxicity. In some embodiments, the antibody treatment, or any combination treatment disclosed herein, is continued for at least about 1 month, at least about 3 months, at least about 6 months, at least about 9 months, at least about 1 year, at least about 18 months, at least about 24 months, at least about 3 years, at least about 5 years, or at least about 10 years.

When used in combinations with other cancer agents, the dosage of an anti-PD-1 antibody can be lowered compared to the monotherapy dose. Dosages of nivolumab that are lower than the typical 3 mg/kg, but not less than 0.001 mg/kg, are subtherapeutic dosages. The subtherapeutic doses of an anti-PD-1 antibody used in the methods herein are higher than 0.001 mg/kg and lower than 3 mg/kg. In some embodiments, a subtherapeutic dose is about 0.001 mg/kg-about 1 mg/kg, about 0.01 mg/kg-about 1 mg/kg, about 0.1 mg/kg-about 1 mg/kg, or about 0.001 mg/kg-about 0.1 mg/kg body weight. In some embodiments, the subtherapeutic dose is at least about 0.001 mg/kg, at least about 0.005 mg/kg, at least about 0.01 mg/kg, at least about 0.05 mg/kg, at least about 0.1 mg/kg, at least about 0.5 mg/kg, or at least about 1.0 mg/kg body weight. Receptor-occupancy data from 15 subjects who received 0.3 mg/kg to 10 mg/kg dosing with nivolumab indicate that PD-1 occupancy appears to be dose-independent in this dose range. Across all doses, the mean occupancy rate was 85% (range, 70% to 97%), with a mean plateau occupancy of 72% (range, 59% to 81%). In some embodiments, 0.3 mg/kg dosing can allow for sufficient exposure to lead to maximal biologic activity. Receptor-occupancy data from 15 subjects who received 0.3 mg/kg to 10 mg/kg dosing with nivolumab indicate that PD-1 occupancy appears to be dose-independent in this dose range. Across all doses, the mean occupancy rate was 85% (range, 70% to 97%), with a mean plateau occupancy of 72% (range, 59% to 81%) (Brahmer et al. (2010) J Clin Oncol 28:3167-75). Thus, 0.3 mg/kg dosing can allow for sufficient exposure to lead to maximal biologic activity.

Although higher nivolumab monotherapy dosing up to about 10 mg/kg every two weeks has been achieved without reaching the maximum tolerated does (MTD), the significant toxicities reported in other trials of checkpoint inhibitors plus anti-angiogenic therapy (see, e.g., Johnson et al. (2013) Cancer Immunol Res 1:373-77; Rini et al. (2011) Cancer 117:758-67) support the selection of a nivolumab dose lower than 10 mg/kg.

In certain embodiments, the dose of an anti-PD-1 antibody or an anti-PD-L1 antibody is a fixed dose in a pharmaceutical composition. In other embodiments, the method of the present invention can be used with a flat dose (a dose given to a patient irrespective of the body weight of the patient). For example, a flat dose of a nivolumab can be about 240 mg. For example, a flat dose of pembrolizumab can be about 200 mg. In some embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is administered at a dose of about 240 mg. In embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is administered at a dose of about 360 mg. In embodiments, the anti-PD-1 antibody or antigen-binding portion thereof is administered at a dose of about 480 mg. In one embodiment, 360 mg of the anti-PD-1 antibody or antigen binding fragment is administered once every 3 weeks. In another embodiment, 480 mg of the anti-PD-1 antibody or antigen binding fragment is administered once every 4 weeks.

In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered at a dose of 0.3 mg/kg, 2 mg/kg, or 10 mg/kg once every 3 weeks. In other embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered at a dose of about 5 mg/kg once about every 3 weeks. In one particular embodiment, the first dose is administered at a dose of at least about 3 mg/kg body weight or 240 mg once about every 2 weeks.

For combinations of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof with other anti-cancer agents, these agents are administered at their approved dosages. Treatment is continued as long as clinical benefit is observed or until unacceptable toxicity or disease progression occurs. Nevertheless, in certain embodiments, the dosages of these anti-cancer agents administered are significantly lower than the approved dosage, i.e., a subtherapeutic dosage, of the agent is administered in combination with the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof. The anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof can be administered at the dosage that has been shown to produce the highest efficacy as monotherapy in clinical trials, e.g., about 3 mg/kg of nivolumab administered once about every three weeks (Topalian et al. (2012) N Engl J Med 366:2443-54; Topalian et al. (2012) Curr Opin Immunol 24:207-12), or at a significantly lower dose, i.e., at a subtherapeutic dose. In one particular embodiment, the first dose of the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is a therapeutic dose and the second dose is a therapeutic dose. In another embodiment, the first dose is a subtherapeutic dose and the second dose is a therapeutic dose. In certain embodiments, the anti-PD-1 antibody or antigen-binding portion thereof and/or the anti-PD-L1 antibody or antigen-binding portion thereof is administered at about 3 mg/kg once about every two weeks.

Actual dosage levels of the active ingredient or ingredients in the pharmaceutical compositions of the present invention can be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being unduly toxic to the patient. The selected dosage level will depend upon a variety of pharmacokinetic factors including the activity of the particular compositions of the present invention employed, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts. A composition of the present invention can be administered via one or more routes of administration using one or more of a variety of methods well known in the art. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results.

In some embodiments, both an anti-PD-1 antibody or antigen-binding portion thereof and an anti-PD-L1 antibody or antigen-binding portion thereof are administered to a patient. The anti-PD-1 antibody or antigen-binding portion thereof and the anti-PD-L1 antibody or antigen-binding portion can be administered concurrently or in sequence (e.g., the anti-PD-1 antibody or antigen-binding portion thereof administered first and the anti-PD-L1 antibody or antigen-binding portion administered second or the anti-PD-L1 antibody or antigen-binding portion administered first and the anti-PD-1 antibody or antigen-binding portion thereof administered second).

In certain aspects of the methods disclosed herein, the subject is administered a first dose of an anti-PD-1 antibody or antigen-binding portion and an anti-PD-L1 antibody or antigen-binding portion thereof, and the expression level of one or more genes, e.g., CTLA-4, TIGIT, PD-L2, or any combination thereof, is measured following the administration of the first dose. In some embodiments, the subject is administered at least two doses, at least three doses, at least four doses, at least five doses, at least six doses, at least seven doses, at least eight doses, at least nine doses, at least ten doses, at least 12 doses, at least 20 doses, or at least 20 doses prior to measuring the expression level of the one or more target genes, e.g., the increased expression of CTLA-4, TIGIT, PD-L2, or any combination thereof.

A subject may continue to receive the anti-PD-1 antibody or antigen-binding portion and/or the anti-PD-L1 antibody or antigen-binding portion thereof for any reasonable duration of time. In some embodiments, the anti-PD-1 antibody or antigen-binding portion or the anti-PD-L1 antibody or antigen-binding portion thereof is administered for as long as a clinical benefit is observed or until unmanageable toxicity or disease progression occurs. In other embodiments, the anti-PD-1 antibody or antigen-binding portion or the anti-PD-L1 antibody or antigen-binding portion thereof is administered for at least about 1 year, at least about 2 years, at least about 3 years, at least about 4 years, at least about 5 years, at least about 6 years, at least about 7 years, at least about 8 years, at least about 9 years, at least about 10 years, at least about 15 years, at least about 20 years, or more than 20 years. In some embodiments, the anti-PD-1 antibody or antigen-binding portion or the anti-PD-L1 antibody or antigen-binding portion thereof is administered until a complete response is observed.

IV. Kits

Also within the scope of the present invention are kits for treating a subject afflicted with a tumor derived from an RCC. Kits typically include a label indicating the intended use of the contents of the kit and instructions for use. The term label includes any writing, or recorded material supplied on or with the kit, or which otherwise accompanies the kit. Accordingly, this disclosure provides a kit for treating a subject afflicted with a tumor derived from an RCC, the kit comprising: (a) an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof; (b) instructions for determining an increased expression of one or more genes, e.g., MICB, PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof, after administration of a first dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof and for administering a second dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof in the methods of claims described herein if the subject exhibits differential expression of CTLA-4, TIGIT, PD-L2, or any combination thereof. In other embodiments, the disclosure provides a kit for treating a subject afflicted with a tumor derived from an RCC, the kit comprising: (a) an anti-PD-1 antibody or antigen-binding portion thereof or an anti-PD-L1 antibody or antigen-binding portion thereof; (b) instructions for determining an expression of one or more genes, e.g., MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, at baseline and for administering a first dose of the anti-PD-1 antibody or antigen-binding portion thereof or the anti-PD-L1 antibody or antigen-binding portion thereof in the methods of claims described herein if the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to the average expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7. In some embodiments, the kit further comprises an agent to determine the differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof prior to administering the second dose and/or an agent to determine the differential expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof at baseline. In certain embodiments, the anti-PD-1 antibody and/or the anti-PD-L1 AB can be co-packaged in unit dosage form. In certain embodiments for treating human patients, the kit comprises an anti-human PD-1 antibody, e.g., nivolumab or pembrolizumab, and/or an anti-human PD-L1 antibody, e.g., BMS-936559, MPDL3280A, MEDI4736, or MSB0010718C. In other embodiments, the kit comprises an anti-human CTLA-4 antibody disclosed herein, e.g., ipilimumab or tremelimumab.

The present invention is further illustrated by the following example, which should not be construed as further limiting. The contents of all references cited throughout this application are expressly incorporated herein by reference.

EXAMPLES Example 1

An open-label, parallel, four-group, phase 1b study of nivolumab (Bristol-Myers Squibb, Lawrenceville, N.J.; Ono Pharmaceutical Company Limited, Osaka City, Japan) to treat mRCC (clean cell) was conducted. Previously treated patients (after anti-angiogenic therapy; n=67) were randomized 1:1:1 to receive one of three nivolumab doses: 0.3 (Arm 1), 2 (Arm 2), or 10 mg/kg (Arm 3); and treatment-naïve patients (n=24) received 10 mg/kg (Arm 4) of nivolumab (FIG. 1). In all groups, nivolumab was administered to the patients as an intravenous infusion on day 1 of a treatment cycle every 3 weeks until the patients showed complete response, progressive disease, intolerable AEs, or withdrawal of consent occurred (FIG. 1). Patients were permitted to continue nivolumab treatment beyond confirmed disease progression if the investigator determined the patient was experiencing clinical benefit and the patient tolerated treatment.

I. Patients

Eligible patients had histologic confirmation of mRCC with a clear-cell component, measurable disease as defined by Response Evaluation Criteria in Solid Tumors (RECIST) v1.1, a Karnofsky performance score of ≥70%, presence of soft-tissue tumor lesions that could be biopsied both at baseline and on-treatment, and adequate organ and marrow function. To be eligible for enrollment in treatment groups 1-3 (previously treated cohorts; Arms 1-3), patients must have been treated with at least one but not more than three previous systemic therapies for RCC with progression occurring following the most recent therapy within 6 months prior to study enrollment (FIG. 1). To be eligible for the treatment-naïve group, patients must not have received any previous systemic therapy in the metastatic or adjuvant setting. Exclusion criteria included active central nervous system metastases within 30 days of study enrollment; active or prior autoimmune disease; active use of systemic corticosteroids; prior malignancy unless complete remission occurred ≥2 years prior to study enrollment; and previous treatment with anti-CTLA-4, anti-PD-1, anti-PD-L1, anti-PD-L2, anti-CD137, anti-CD40, or anti-OX40 antibodies.

II. Study Assessments A. Objectives and Assessments

The primary objective of this study was to investigate the pharmacodynamic immunomodulatory activity of nivolumab on CD4+ and CD8+ tumor-associated lymphocytes, and serum chemokines CXCL9 and CXL10 in patients with clear-cell mRCC. Secondary objectives were to assess the efficacy, safety, and tolerability of nivolumab. Exploratory objectives included analyses of additional serum-soluble factors in serum, gene expression profiling in the tumor and whole blood, PD-L1 expression by tumor membrane staining, clinical activity according to PD-L1 expression prior to treatment, and receptor occupancy.

Patients were evaluated for response (RECIST v1.1) every 6 weeks for the first 12 months from randomization, then every 12 weeks until documented disease progression. Patients who discontinued treatment for reasons other than tumor progression continued to have tumor assessments according to the treatment schedule.

Patients were required to provide fresh biopsies both at screening and on treatment as a condition of protocol participation. Tumor sites selected for biopsy must not have received previous radiation therapy. It was preferred that patients have at least one soft-tissue lesion large enough to undergo repeat core needle biopsies (one biopsy at baseline and one biopsy at cycle 2 day 8). However, patients may also have had two distinct soft-tissue lesions eligible for core needle or excisional biopsies. One lesion was to be biopsied at baseline and the other was to be biopsied at cycle 2 day 8.

B. Biomarker Assessments

Assessment of immune cells was performed by using two validated multiplex IHC assays provided by Mosaic Laboratories (Lake Forest, Calif.) on formalin-fixed, paraffin-embedded sections. The assays selected were one dual stain, CD3+/CD8+, and one triple stain, CD3+/CD4+/FOXP3+. Each multiplex IHC assay was designed and validated to be compatible with Clinical Laboratory Improvement Amendments guideline class I test validation. A representative 20× field of staining was spectrally imaged using the NUANCE® Multispectral Imaging System with software v.2.4.0 (Caliper Life Sciences, Hopkinton, Mass.) attached to a NIKON® 90i microscope. The multispectral image was acquired between 420 and 720 nm using 20-nm wavelength steps. Image cubes were analyzed using INFORM® software v1.2 (Caliper Life Sciences). Image cubes were unmixed using the spectral absorbance patterns for each chromogen and hematoxylin.

Nivolumab binding to PD-1 molecules on circulating T cells was investigated by flow cytometric analysis of serially collected blood samples. The assay was optimized from the receptor occupancy assay as described previously (Brahmer et al. (2010) J Clin Oncol 28:3167-75). Briefly, PD-1 occupancy by infused nivolumab was estimated as the ratio of the percent of total T cells, CD4+ T cells, and CD8+ T cells stained with antidrug antibody (anti-huIgG4) after in vitro saturation with isotype control antibody (indicating in vivo binding) to that observed after nivolumab saturation (indicating total available binding sites). To obtain these measures, individual aliquots of each whole blood sample were preincubated (30 minutes at 4° C.) with a saturating concentration (50 μg/ml) of either isotype control or nivolumab, washed extensively, and then co-stained with anti-CD3 PerCP, anti-CD4 FITC, anti-CD8 APC, and murine anti-huIgG4 PE (SouthernBiotech, Birmingham, Ala.).

The biopsies obtained from metastatic lesions at baseline and cycle 2 day 8 were used for the quantification of tumor-associated lymphocytes, for evaluation of the expression of PD-L1 and PD-1 proteins, and for evaluation of gene expression. IHC (Mosaic Laboratories) was used to assess the number and composition of tumor-associated lymphocytes, including CD4+ and CD8+ cells (Table 1). The expression of PD-L1 on the surface of tumor cells was assessed in these biopsies and in archival samples, when available, at a central laboratory with the use of an automated IHC assay (Bristol-Myers Squibb/Dako IHC assay using the 28-8 antibody), as described previously (Sznol et al. (2014) J Clin Oncol 32:Abstract LBA9003). The level of PD-L1 expression was determined by the cell-surface PD-L1 staining of any intensity in a section containing at least 100 tumor cells that could be evaluated. RNA was extracted from the fresh biopsies in parallel to IHC and also from whole blood at cycle 1 day 1 (prior to nivolumab infusion), cycle 1 day 2, and cycle 2 day 8. RNA was labeled by WT-Pico OVATION® (NuGEN, San Carlos, Calif.). Gene expression profiling was performed using the HG-U219 array plate on the GENETITAN® platform (Affymetrix, Santa Clara, Calif.). The robust multi-array average (RMA) algorithm (Irizarry et al. (2003) Nucleic Acids Res 31:e15) was used to establish intensity values for each of 18,562 loci (BrainArray v.10) (Dai et al. (2005) Nucleic Acids Res 33:e175). Data have been deposited in ArrayExpress (E-MTAB-3218 and E-MTAB-3219).

TABLE 1 Assessments of Immunomodulatory Activity. Analysis Sample Assay Time Points PD-L1 expression FFPE tumor IHC (BMS/Dako; Baseline biopsy 28-8 antibody) Soluble factors Serum LUMINX ™ (Myriad Baseline, RBM) C2D8 Gene expression Tumor biopsy AFFYMETRIX ® Baseline, profiling Human Genome U219 C2D8 T-cell receptor Frozen tumor IMMUNOSEQ ™ Baseline, sequencing biopsy, PBMC (Adaptive C2D8 Biotechnologies) Note Baseline refers to tumor biopsies collected during screening or peripheral bold collected on day 1 of the first cycle, prior to nivolumab infusion. C2D8, cycle 2 day 8; FFPE, formalin-fixed, paraffin-embedded; PBMC, peripheral blood mononuclear cells.

The assessment of serum chemokines (CXCL9, CXCL10) and other serum-soluble factors (Table 9) at baseline, cycle 1 day 1, cycle 2 day 1, cycle 2 day 8, and cycle 4 day 1 was performed for all treated patients for whom serum was available using a multiplex panel based on LUMINEX® technology (Myriad Rules-Based Medicine, Austin, Tex.).

TABLE 2 108 Genes From an Analysis of Tumor Biopsies Baseline: C2D8: C2D8 v. HUGO P value for Mean Mean Baseline: Probeset ENTREZ Gene baseline v. RMA RMA Fold (BrainArray v.10) Gene ID Symbol C2D8 value value Change BrAr: LOC118932_at LOC118932 ANKRD22 0.0006207 3.73 4.3 1.48 BrAr: LOC54518_at LOC54518 APBB1IP 0.00018251 8.4 8.83 1.34 BrAr: LOC200316_at LOC200316 APOBEC3F 0.00010417 4.43 4.93 1.42 BrAr: LOC60489_at LOC60489 APOBEC3G 0.00135835 5.77 6.32 1.46 BrAr: LOC80833_at LOC80833 APOL3 0.00151848 8.11 8.58 1.39 BrAr: LOC80830_at LOC80830 APOL6 0.00408546 5.15 5.53 1.3 BrAr: LOC116984_at LOC116984 ARAP2 0.00119885 4.93 5.37 1.36 BrAr: LOC283897_at LOC283897 C16orf54 0.0094305 5.84 6.42 1.5 BrAr: LOC132720_at LOC132720 C4ORF32 0.00690996 5.01 5.41 1.32 BrAr: LOC834_at LOC834 CASP1 0.00036764 6.35 6.76 1.33 BrAr: LOC6351_at LOC6351 CCL4 0.00966536 7.88 8.33 1.37 BrAr: LOC6352_at LOC6352 CCL5 0.00164617 6.82 7.65 1.77 BrAr: LOC919_at LOC919 CD247 0.00434502 3.8 4.32 1.43 BrAr: LOC29126_at LOC29126 CD274 0.00151105 3.79 4.18 1.31 BrAr: LOC915_at LOC915 CD3D 0.00637029 5.48 6.21 1.66 BrAr: LOC916_at LOC916 CD3E 0.00891231 4.76 5.54 1.72 BrAr: LOC917_at LOC917 CD3G 0.00874864 5.3 6 1.62 BrAr: LOC962_at LOC962 CD48 0.00951571 7.06 7.75 1.61 BrAr: LOC963_at LOC963 CD53 0.0061421 7.31 7.75 1.36 BrAr: LOC969_at LOC969 CD69 0.00398662 3.47 4.1 1.55 BrAr: LOC971_at LOC971 CD72 0.00320178 2.71 3.18 1.39 BrAr: LOC925_at LOC925 CD8A 0.0024245 5.45 6.19 1.67 BrAr: LOC926_at LOC926 CD8B 0.00505758 2.63 3.17 1.46 BrAr: LOC160364_at LOC160364 CLEC12A 0.00277043 3.65 4.12 1.39 BrAr: LOC7373_at LOC7373 COL14A1 0.00689524 6.63 6.25 0.77 BrAr: LOC1307_at LOC1307 COL16A1 0.0007086 4.95 4.55 0.76 BrAr: LOC11151_at LOC11151 CORO1A 0.00977025 4.41 4.79 1.3 BrAr: LOC8530_at LOC8530 CST7 0.00163984 5.57 6.37 1.74 BrAr: LOC1493_at LOC1493 CTLA4 0.0083113 3.36 3.77 1.33 BrAr: LOC1520_at LOC1520 CTSS 0.00510613 8.01 8.45 1.35 BrAr: LOC6373_at LOC6373 CXCL11 0.00144838 4.68 5.63 1.93 BrAr: LOC4283_at LOC4283 CXCL9 0.00079598 7.1 8.38 2.43 BrAr: LOC10663_at LOC10663 CXCR6 8.4691E−05 5.16 5.93 1.71 BrAr: LOC80231_at LOC80231 CXORF21 0.00929267 3.01 3.44 1.34 BrAr: LOC27071_at LOC27071 DAPP1 0.0022226 3.92 4.42 1.41 BrAr: LOC1734_at LOC1734 DIO2 0.00979853 4.66 4.14 0.7 BrAr: LOC81704_at LOC81704 DOCK8 0.00102282 5.03 5.43 1.32 BrAr: LOC94240_at LOC94240 EPSTI1 0.00022911 5.63 6.22 1.51 BrAr: LOC125704_at LOC125704 FAM69C 0.00014377 3.67 3.27 0.76 BrAr: LOC2207_at LOC2207 FCER1G 0.00055515 8.61 9.05 1.35 BrAr: LOC10875_at LOC10875 FGL2 0.00314134 7.21 7.65 1.35 BrAr: LOC2533_at LOC2533 FYB 0.00755475 6.66 7.13 1.39 BrAr: LOC2633_at LOC2633 GBP1 5.3598E−05 5.87 6.72 1.81 BrAr: LOC115361_at LOC115361 GBP4 0.00020926 6.08 6.76 1.6 BrAr: LOC115362_at LOC115362 GBPS 0.00017365 6.13 7.06 1.9 BrAr: LOC2643_at LOC2643 GCH1 0.00041451 6.6 7.25 1.57 BrAr: LOC29909_at LOC29909 GPR171 0.00072124 4.68 5.42 1.68 BrAr: LOC3001_at LOC3001 GZMA 0.00054429 7.54 8.32 1.72 BrAr: LOC3002_at LOC3002 GZMB 0.0041206 5.16 5.99 1.78 BrAr: LOC2999_at LOC2999 GZMH 0.00020686 5.85 6.81 1.94 BrAr: LOC29851_at LOC29851 ICOS 0.0041205 4.1 4.57 1.39 BrAr: LOC3620_at LOC3620 IDO1 0.00105399 4.74 5.76 2.02 BrAr: LOC64135_at LOC64135 IFIH1 0.00633078 6.53 6.91 1.31 BrAr: LOC3433_at LOC3433 IFIT2 0.0009791 6.25 6.68 1.35 BrAr: LOC8519_at LOC8519 IFITM1 0.00329708 8.06 8.47 1.33 BrAr: LOC3458_at LOC3458 IFNG 0.00252908 2.58 3.14 1.47 BrAr: LOC3488_at LOC3488 IGFBP5 0.00686955 8.88 8.41 0.72 BrAr: LOC10261_at LOC10261 IGSF6 0.00738051 7.64 8.05 1.32 BrAr: LOC22806_at LOC22806 IKZF3 0.00348126 4.3 5.11 1.76 BrAr: LOC3553_at LOC3553 IL1B 0.00541195 4.48 4.86 1.3 BrAr: LOC3560_at LOC3560 IL2RB 0.00461433 4.18 4.82 1.56 BrAr: LOC3561_at LOC3561 IL2RG 0.00616889 6.25 6.99 1.66 BrAr: LOC3659_at LOC3659 IRF1 4.7581E−06 5.05 5.59 1.46 BrAr: LOC3689_at LOC3689 ITGB2 0.00726197 7.44 7.95 1.42 BrAr: LOC3702_at LOC3702 ITK 0.00081966 2.89 3.36 1.39 BrAr: LOC3759_at LOC3759 KCNJ2 0.0098923 5.87 6.28 1.33 BrAr: LOC3820_at LOC3820 KLRB1 0.0017051 4.05 4.57 1.43 BrAr: LOC3824_at LOC3824 KLRD1 0.00602459 4.33 4.77 1.36 BrAr: LOC10219_at LOC10219 KLRG1 0.00509516 4.13 4.6 1.39 BrAr: LOC51056_at LOC51056 LAP3 0.00062969 7.18 7.65 1.38 BrAr: LOC3936_at LOC3936 LCP1 0.00788663 7.8 8.33 1.45 BrAr: LOC3957_at LOC3957 LGALS2 0.00048367 7.7 8.37 1.59 BrAr: LOC10859_at LOC10859 LILRB1 0.00234176 4.14 4.62 1.39 BrAr: LOC4065_at LOC4065 LY75 0.00385138 5.56 5.99 1.35 BrAr: LOC55686_at LOC55686 MREG 0.0024365 5.82 6.41 1.51 BrAr: LOC3071_at LOC3071 NCKAP1L 0.0088131 4.18 4.75 1.48 BrAr: LOC4818_at LOC4818 NKG7 0.00083844 6.27 6.97 1.62 BrAr: LOC53829_at LOC53829 P2RY13 1.4924E−05 6 6.54 1.46 BrAr: LOC56937_at LOC56937 PMEPA1 0.00349819 7.06 6.65 0.75 BrAr: LOC5551_at LOC5551 PRF1 0.00344285 4.11 4.7 1.5 BrAr: LOC5579_at LOC5579 PRKCB 0.00760977 4.05 4.54 1.4 BrAr: LOC5698_at LOC5698 PSMB9 0.00174273 9.27 9.65 1.31 BrAr: LOC9050_at LOC9050 PSTPIP2 2.3187E−05 3.51 4.28 1.71 BrAr: LOC5784_at LOC5784 PTPN14 0.00924443 5.31 4.91 0.76 BrAr: LOC5880_at LOC5880 RAC2 0.00321482 5.86 6.41 1.46 BrAr: LOC5920_at LOC5920 RARRES3 0.0044999 9.51 9.94 1.34 BrAr: LOC64108_at LOC64108 RTP4 0.00041451 4.67 5.11 1.36 BrAr: LOC219285_at LOC219285 SAMD9L 0.00853322 5.6 5.99 1.31 BrAr: LOC64092_at LOC64092 SAMSN1 0.0037497 5.63 6.03 1.32 BrAr: LOC54440_at LOC54440 SASH3 0.00070534 3.98 4.49 1.42 BrAr: LOC388325_at LOC388325 SCIMP 0.00491723 4.83 5.37 1.45 BrAr: LOC6401_at LOC6401 SELE 0.00242864 3.65 3.21 0.73 BrAr: LOC4068_at LOC4068 SH2D1A 0.00569087 3.28 3.85 1.49 BrAr: LOC57823_at LOC57823 SLAMF7 0.00970256 5.22 6.02 1.74 BrAr: LOC6772_at LOC6772 STAT1 0.00462175 8.1 8.6 1.42 BrAr: LOC6775_at LOC6775 STAT4 0.0051167 3.92 4.37 1.37 BrAr: LOC6890_at LOC6890 TAP1 0.00475158 6.41 6.8 1.31 BrAr: LOC57451_at LOC57451 TENM2 0.00026164 2.73 2.29 0.73 BrAr: LOC387357_at LOC387357 THEMIS 0.00431695 3.89 4.48 1.51 BrAr: LOC51311_at LOC51311 TLR8 0.00447705 4.77 5.24 1.39 BrAr: LOC28755_at LOC28755 TRAC 0.00397501 6.07 6.89 1.76 BrAr: LOC50852_at LOC50852 TRAT1 0.00410059 3.66 4.35 1.61 BrAr: LOC10537_at LOC10537 UBD 0.00031032 8.92 9.82 1.87 BrAr: LOC7351_at LOC7351 UCP2 0.00078162 7.18 7.63 1.36 BrAr: LOC7409_at LOC7409 VAV1 0.00355556 4.48 4.94 1.37 BrAr: LOC8875_at LOC8875 VNN2 0.00439216 4.63 5.07 1.36 BrAr: LOC7453_at LOC7453 WARS 0.00106922 7 7.58 1.5 BrAr: LOC79413_at LOC79413 ZBED2 0.0011301 2.63 3.18 1.47 Note: These are genes for which the null hypothesis was rejected and the change over time averaged over treatment groups was >1.3-fold.

Patients who received the study drug were included in the safety population. Safety assessments were conducted at every visit and were evaluated according to the National Cancer Institute Common Terminology Criteria for Adverse Events, version 4.0 (National Cancer Institute, 2009). Safety was assessed by the incidence of adverse events (AEs) and select AEs that may be related to the mechanism of action of nivolumab. Select AEs of interest were defined as events with potential immunologic causes and those that required more frequent monitoring or intervention with immune suppression.

C. Statistical Analysis

This study was not designed to statistically test a specific hypothesis; therefore the sample size was not based on statistical power calculations. The study was designed to explore the pharmacodynamic effects of nivolumab in patients with mRCC, and using this information, to generate hypotheses for testing of selected biomarkers in subsequent clinical studies.

Efficacy analyses included best overall response (complete response (CR), partial response (PR), stable disease (SD), progressive disease (PD)), Progression Free Survival (PFS), and overall survival (OS), as well as objective response rate (ORR), which was the proportion of patients whose best response was a CR or PR. The 95% CIs for assessment of ORR were estimated using the Clopper-Pearson method (Clopper et al. (1934) Biometrika 26:404-13). PFS was defined as the time from first dosing date to the date of first documented disease progression. PFS and OS functions were estimated by the Kaplan-Meier method with 95% CIs estimated using Greenwood's formula (Brookmeyer et al. (1982) Biometrics 38:29-41).

The pharmacodynamic effects of nivolumab on tumor-associated lymphocytes and serum chemokines and in tumors were described using summary statistics and changes or percent changes from baseline tabulated by cycle, visit, and dose. Analyses of the relationship of gene expression to pharmacodynamic parameters (treatment group and time on study) were based on an extended linear model, fit by restricted maximum likelihood (NLME version 3.1-109 under R 3.0.1 for Linux) (Pinheiro et al. (2013) R package version 3.1-109 [Computer software]). For blood samples, the model included fixed effects of treatment group and time on study as categorical variables, and treatment-by-time on study interactions. For tumor biopsy samples, the model also included fixed effects of process batch and sex (the latter because women were not equally represented in samples from each trial treatment group). Within-patient correlations were modeled by a spatial exponential structure with Euclidean distance. A multi-contrast conditional F test was used to compare the null hypothesis that all time-related fixed-effect parameters were zero versus an alternative hypothesis that gene expression changed over time in at least one treatment group. The q value of each test (expected proportion of false positives incurred at that p value) was also estimated. Results presented are genes for which this null hypothesis was rejected (p for time on study <0.01), and the change over time averaged over treatment groups was >1.3-fold (biopsy; 108 genes in Table 2) or >1.2-fold (blood; 59 genes in Table 3). Analyses of the relationships of gene expression to Response parameters (Maximal reduction in tumor burden of >20%) were based on an extended linear model, fit by restricted maximum likelihood (NLME version 3.1-109 under R 3.0.1 for Linux) (Pinheiro et al. (2013) R package version 3.1-109 [Computer software]). The model included fixed effects of Response, time on study, process batch and sex as categorical variables, and Response-by-time on study interactions. Within-patient correlations were modeled by a spatial exponential structure with Euclidean distance. A multi-contrast conditional F test was used to compare the null hypothesis that all Response-related fixed-effect parameters were zero versus an alternative hypothesis that gene expression differed at at least one time in at least one Response group. The q value of each test (expected proportion of false positives incurred at that p value) was also estimated. Results presented are genes for which this null hypothesis was rejected (p for a difference between Response groups at any time point <0.05), and the difference between Response groups at a given time met p<0.01 and was >1.25-fold (311 genes at baseline, Table 6A; 779 genes at C1D28, Table 7A). For a subset of the 779 genes, the interaction between Response and time also met p<0.01 and the change upon treatment in Responders was >1.25-fold (56 genes in Table 8A). The sets of transcripts meeting each of the above significance criteria were evaluated for enrichment (Tilford et al. 2009, Gene set enrichment analysis, In Protein Networks and Pathways, Nikolsky, Y. and Bryant, J. (Eds.), New York: Humana Press, pp. 99-122) (p values provided were Bonferroni corrected) of 1,539 genes from immune cell lineages (Abbas et al. (2005) Genes Immun 6:319-31) and for biological impact (MetaCore; Thomson Reuters, New York, N.Y.).

TABLE 3 59 Transcripts From Whole Blood Analysis. C1D1: C1D2: C1D2 v. P value for Mean Mean C1D1: Probeset ENTREZ HUGO Gene C1D2 v. RMA RMA Fold (BrainArray v.10) Gene ID Symbol C1D1 value value Change BrAr: LOC3983_at LOC3983 ABLIM1 4.75997E−05 4.67 4.39 0.82 BrAr: LOC9447_at LOC9447 AIM2 0.0014429 4.7 5.02 1.25 BrAr: LOC29123_at LOC29123 ANKRD11 0.004165336 6.64 6.32 0.81 BrAr: LOC118932_at LOC118932 ANKRD22 3.93174E−05 3.21 3.52 1.24 BrAr: LOC1236_at LOC1236 CCR7 2.93852E−05 7.88 7.41 0.72 BrAr: LOC939_at LOC939 CD27 1.28677E−05 6.3 5.97 0.79 BrAr: LOC917_at LOC917 CD3G 0.005433463 6.09 5.63 0.73 BrAr: LOC91351_at LOC91351 DDX60L 5.63444E−09 6.8 7.1 1.23 BrAr: LOC1975_at LOC1975 EIF4B 0.005759727 5.09 4.74 0.78 BrAr: LOC94240_at LOC94240 EPSTI1 9.11328E−09 4.88 5.49 1.53 BrAr: LOC51513_at LOC51513 ETV7 6.46465E−05 2.72 3.02 1.23 BrAr: LOC441168_at LOC441168 FAM26F 2.57221E−07 4.75 5.1 1.27 BrAr: LOC26270_at LOC26270 FBXO6 4.64598E−10 4.08 4.53 1.37 BrAr: LOC2272_at LOC2272 FHIT 0.004291588 5.06 4.77 0.82 BrAr: LOC2633_at LOC2633 GBP1 2.4785E−10 4.33 4.9 1.48 BrAr: LOC115361_at LOC115361 GBP4 3.84104E−06 2.87 3.15 1.21 BrAr: LOC115362_at LOC115362 GBP5 1.12749E−09 5.15 5.69 1.46 BrAr: LOC2643_at LOC2643 GCH1 2.83232E−08 4.25 4.61 1.29 BrAr: LOC2710_at LOC2710 GK 0.000283034 4.45 4.81 1.29 BrAr:LOC2745_at LOC2745 GLRX 0.001989618 5.55 5.81 1.21 BrAr: LOC3430_at LOC3430 IFI35 1.64598E−05 6.18 6.52 1.27 BrAr: LOC10561_at LOC10561 IFI44 0.00021054 3.86 4.19 1.25 BrAr: LOC2537_at LOC2537 IFI6 0.000341067 6.34 6.66 1.25 BrAr: LOC64135_at LOC64135 IFIH1 0.002562623 5.05 5.32 1.2 BrAr: LOC3434_at LOC3434 IFIT1 2.30102E−05 6.22 6.65 1.35 BrAr: LOC3433_at LOC3433 IFIT2 5.89582E−05 5.08 5.38 1.23 BrAr: LOC3437_at LOC3437 IFIT3 0.002092781 6.56 6.85 1.23 BrAr: LOC3575_at LOC3575 IL7R 5.15074E−07 7.84 7.3 0.69 BrAr: LOC3665_at LOC3665 IRF7 1.9346E−06 7.21 7.56 1.27 BrAr: LOC9636_at LOC9636 ISG15 0.001134979 6.47 6.76 1.23 BrAr: LOC51056_at LOC51056 LAP3 0.003108231 2.77 3.11 1.26 BrAr: LOC100128751_at LOC100128751 LOC100128751 0.008038775 6.23 5.93 0.81 BrAr: LOC100131541_at LOC100131541 LOC100131541 0.005861658 4.52 4.1 0.74 BrAr: LOC4118_at LOC4118 MAL 7.17596E−06 6.53 6.24 0.82 BrAr: LOC4775_at LOC4775 NFATC3 0.000709543 6.33 5.96 0.77 BrAr: LOC57185_at LOC57185 NIPAL3 0.001814472 4.43 4.08 0.78 BrAr: LOC9934_at LOC9934 P2RY14 5.87145E−05 3.3 3.73 1.35 BrAr: LOC286530_at LOC286530 P2RY8 0.005584607 7.21 6.93 0.82 BrAr: LOC54625_at LOC54625 PARP14 2.23537E−07 4.12 4.42 1.24 BrAr: LOC83666_at LOC83666 PARP9 1.66909E−05 5.27 5.63 1.28 BrAr: LOC5359_at LOC5359 PLSCR1 3.57775E−07 5.9 6.26 1.29 BrAr: LOC5423_at LOC5423 POLB 0.000820428 5.98 6.24 1.2 BrAr: LOC9050_at LOC9050 PSTPIP2 9.27591E−13 5.6 6.02 1.34 BrAr: LOC55647_at LOC55647 RAB20 0.000477973 3.3 3.61 1.24 BrAr: LOC6095_at LOC6095 RORA 0.007747422 5.01 4.69 0.8 BrAr: LOC64108_at LOC64108 RTP4 0.000207057 3.23 3.51 1.21 BrAr: LOC219285_at LOC219285 SAMD9L 2.81577E−05 4.33 4.65 1.24 BrAr: LOC9997_at LOC9997 SCO2 2.04163E−05 7.18 7.63 1.37 BrAr: LOC710_at LOC710 SERPING1 0.001824018 3.05 3.4 1.27 BrAr: LOC6772_at LOC6772 STAT1 8.03115E−10 4.89 5.29 1.32 BrAr: LOC6890_at LOC6890 TAP1 3.26126E−05 7.72 8.01 1.22 BrAr: LOC7130_at LOC7130 TNFAIP6 3.48335E−05 7.18 7.58 1.31 BrAr: LOC28755_at LOC28755 TRAC 7.80813E−05 8.32 7.98 0.79 BrAr: LOC28638_at LOC28638 TRBC2 5.36988E−05 9.33 9.05 0.82 BrAr: LOC10346_at LOC10346 TRIM22 1.69393E−06 5.42 5.82 1.32 BrAr: LOC1890_at LOC1890 TYMP 0.002083458 5.8 6.15 1.27 BrAr: LOC9246_at LOC9246 UBE2L6 2.71549E−10 7.9 8.26 1.28 BrAr: LOC10791_at LOC10791 VAMPS 7.41239E−05 5.92 6.3 1.3 BrAr: LOC7453_at LOC7453 WARS 0.000887265 6.67 7.01 1.26 Note: These are transcripts for which the null hypothesis was rejected and the change over time averaged over treatment groups was >1.2-fold.

Within the analyses of the relationship of gene expression to pharmacodynamic parameters (treatment group and time on study) possible treatment group-specific effects were examined. Among genes where the null hypothesis was rejected (p for time on study, <0.01), a second multi-contrast test of all time-by-treatment interaction parameters was used to test whether the pattern of expression change differed between at least two treatment groups. If this null hypothesis was rejected (p<0.01 for interaction between dose and time on study or between previous treatment status and time on study), then we examined the effect size in each treatment group. Genes for which the change over time for at least one treatment group was >1.3-fold (biopsy; 37 probesets) or >1.2-fold (blood; 24 probesets) are presented in Tables 4 and 5. In all cases, the change over time for at least two of the other treatment groups did not meet those criteria.

TABLE 4 Genes From an Analysis of Tumor Biopsies With >1.3-fold Differences Between Treatment Groups Over Time. P value P value for P value for change for change upon upon treatment HUGO change treatment differing between Probeset ENTREZ Gene upon differing between pretreated and (BrainArray v.10) Gene ID Symbol treatment Dose groups Naïve Comment 139886_at LOC139886 SPIN4 0.000227 0.909 0.000207 Possible effect of Pretreatment 165215_at LOC165215 FAM171B 0.000309 0.306 0.00119 Possible effect of Pretreatment 677841_at LOC677841 SNORA74B 0.000915 0.289 0.00276 Possible effect of Pretreatment 158405_at LOC158405 KIAA1958 0.00116 0.677 0.00843 Possible effect of Pretreatment 81839_at LOC81839 VANGL1 0.00126 0.225 0.00993 Possible effect of Pretreatment 7056_at LOC7056 THBD 0.00158 0.861 0.00528 Possible effect of Pretreatment 80256_at LOC80256 FAM214B 0.00163 0.758 0.00298 Possible effect of Pretreatment 29984_at LOC29984 RHOD 0.00244 0.591 0.00417 Possible effect of Pretreatment 283899_at LOC283899 INO80E 0.00844 0.72 0.00597 Possible effect of Pretreatment 838_at LOC838 CASP5 0.0000112 0.00368 0.224 Possible effect of Dose 22934_at LOC22934 RPIA 0.0000468 0.000416 0.589 Possible effect of Dose 7920_at LOC7920 ABHD16A 0.0000576 0.000157 0.591 Possible effect of Dose 649_at LOC649 BMP1 0.0000881 0.00834 0.123 Possible effect of Dose 5136_at LOC5136 PDE1A 0.00013 0.000293 0.705 Possible effect of Dose 441631_at LOC441631 TSPAN11 0.000144 0.00141 0.184 Possible effect of Dose 57167_at LOC57167 SALL4 0.000197 0.00235 0.785 Possible effect of Dose 57451_at LOC57451 TENM2 0.000262 0.00167 0.2 Possible effect of Dose 4131_at LOC4131 MAP1B 0.000373 0.00715 0.0496 Possible effect of Dose 5793_at LOC5793 PTPRG 0.000387 0.00696 0.0644 Possible effect of Dose 6750_at LOC6750 SST 0.00044 0.00744 0.959 Possible effect of Dose 131375_at LOC131375 LYZL4 0.000503 0.0000613 0.17 Possible effect of Dose 23608_at LOC23608 MKRN1 0.000583 0.00243 0.385 Possible effect of Dose 64175_at LOC64175 LEPRE1 0.000584 0.00701 0.468 Possible effect of Dose 257019_at LOC257019 FRMD3 0.000625 0.00202 0.392 Possible effect of Dose 253512_at LOC253512 SLC25A30 0.000641 0.00153 0.266 Possible effect of Dose 58484_at LOC58484 NLRC4 0.000701 0.00578 0.387 Possible effect of Dose 8458_at LOC8458 TTF2 0.000977 0.00307 0.249 Possible effect of Dose 80381_at LOC80381 CD276 0.000978 0.000694 0.821 Possible effect of Dose 5291_at LOC5291 PIK3CB 0.000992 0.00198 0.355 Possible effect of Dose 3908_at LOC3908 LAMA2 0.00124 0.00746 0.25 Possible effect of Dose 6531_at LOC6531 SLC6A3 0.00141 0.00586 0.116 Possible effect of Dose 51257_at LOC51257 MAR2 0.00162 0.00738 0.0142 Possible effect of Dose 221656_at LOC221656 KDM1B 0.00166 0.00867 0.963 Possible effect of Dose 3956_at LOC3956 LGALS1 0.00173 0.000595 0.161 Possible effect of Dose 84243_at LOC84243 ZDHHC18 0.00179 0.00933 0.252 Possible effect of Dose 5654_at LOC5654 HTRA1 0.00181 0.00388 0.781 Possible effect of Dose 4920_at LOC4920 ROR2 0.00186 0.000622 0.469 Possible effect of Dose Note: Thirty-seven probesets identified from gene expression analysis.

TABLE 5 Genes From Whole Blood Analysis With >1.2-fold Differences Between Treatment Groups Over Time. P value for P value for change upon change upon treatment treatment differing Probeset HUGO P value for differing between (BrainArray ENTREZ Gene change upon between pretreated v.10) Gene ID Symbol treatment Dose groups and Naïve Comment 3301_at LOC3301 DNAJA1 0.000300892 0.00283273 0.1319663 Possible effect of Dose 27247_at LOC27247 NFU1 0.003282889 0.001166246 0.01694071 Possible effect of Dose 28227_at PPP2R3B || ? 0.006291189 0.006389651 0.06670232 Possible effect of Dose || ? 283537_at LOC283537 SLC46A3 0.005223015 0.003790012 0.06725309 Possible effect of Dose 6643_at LOC6643 SNX2 0.000891442 0.000328151 0.04873944 Possible effect of Dose 379013_at RNF138 || 0.005091024 0.000976717 0.2653985 RNF138P1 Possible effect of Dose 55855_at FAM45B || 0.001326355 0.001402364 0.04572821 Possible effect of Dose FAM45A 30011_at LOC30011 SH3KBP1 0.00376672 0.007403809 0.01968723 Possible effect of Dose 23112_at LOC23112 TNRC6B 0.001041506 0.004713658 0.01089389 Possible effect of Dose 23741_at LOC23741 EID1 0.004571983 0.005961323 0.064752 Possible effect of Dose 23215_at LOC23215 PRRC2C 0.008805884 0.009225187 0.01164823 Possible effect of Dose 57466_at LOC57466 SCAF4 0.005837828 0.003790088 0.01926408 Possible effect of Dose 100507117_at LOC100507117 ASAP1-IT2 0.009482807 0.006106619 0.006915612 Possible effect of Dose Possible effect of 4775_at LOC4775 NFATC3 0.000709543 0.02451703 0.007846956 Pretreatment Possible effect of 100507117_at LOC100507117 ASAP1-IT2 0.009482807 0.006106619 0.006915612 Pretreatment Possible effect of 23157_at LOC23157 0.0014221 0.2044598 0.004195466 Pretreatment Possible effect of 54737_at LOC54737 MPHOSPH8 0.004196599 0.04784359 0.005009904 Pretreatment Possible effect of 54876_at LOC54876 DCAF16 1.1088E−05 0.02246931 0.000732451 Pretreatment Possible effect of 51176_at LOC51176 LEF1 0.002074846 0.4212703 0.007699788 Pretreatment Possible effect of 26999_at LOC26999 CYFIP2 0.00204136 0.3130331 0.00867614 Pretreatment Possible effect of 81539_at LOC81539 SLC38A1 0.000962059 0.08678283 0.007378195 Pretreatment Possible effect of 9214_at LOC9214 FAIM3 0.001082093 0.5771362 0.008717745 Pretreatment Possible effect of 54900_at LOC54900 LAX1 0.001028967 0.3447576 0.008016235 Pretreatment Possible effect of 3615_at LOC3615 IMPDH2 0.008047956 0.5363073 0.008885895 Pretreatment Note: Twenty-four probesets identified from gene expression analysis.

TABLE 6A Genes From an Analysis of Tumor Biopsies With ≥1.2-fold or ≤0.8-fold Differences Between Treatment at Baseline. No P value for Response: Response: Response v. No Response v. No Mean RMA Mean RMA response: Fold Probeset (BrainArray ENTREZ Gene HUGO Gene Response at value at value at difference at v.10) ID Symbol baseline baseline baseline baseline BrAr:LOC1_at LOC1 A1BG 0.002439879 2.34 2.7 1.28 BrAr:LOC8647_at LOC8647 ABCB11 0.009042188 2.08 2.41 1.26 BrAr:LOC10152_at LOC10152 ABI2 0.002010763 6.7 6.28 0.74 BrAr:LOC11174_at LOC11174 ADAMTS6 1.69594E−06 2.25 2.59 1.26 BrAr:LOC10939_at LOC10939 AFG3L2 0.007003315 6.23 5.69 0.68 BrAr:LOC177_at LOC177 AGER 0.000612783 3.09 3.45 1.29 BrAr:LOC9447_at LOC9447 AIM2 0.000486717 4.68 6.62 3.82 BrAr:LOC338692_at LOC338692 ANKRD13D 0.000854153 4.12 4.5 1.31 BrAr:LOC122416_at LOC122416 ANKRD9 0.00839715 3.61 3.99 1.3 BrAr:LOC10947_at LOC10947 AP3M2 0.004540524 4.6 4.15 0.73 BrAr:LOC164668_at LOC164668 APOBEC3H 0.000373208 3.44 3.81 1.28 BrAr:LOC351_at LOC351 APP 0.003579009 10.52 10.09 0.74 BrAr:LOC394_at LOC394 ARHGAP5 0.003585724 5.57 5.05 0.7 BrAr:LOC64333_at LOC64333 ARHGAP9 0.001948117 3.8 4.56 1.7 BrAr:LOC128272_at LOC128272 ARHGEF19 0.000141249 4.01 4.4 1.31 BrAr:LOC51008_at LOC51008 ASCC1 0.003067675 6.6 6.15 0.73 BrAr:LOC433_at LOC433 ASGR2 0.008844586 3.34 3.79 1.36 BrAr:LOC9212_at LOC9212 AURKB 0.00323879 4.39 4.75 1.29 BrAr:LOC10538_at LOC10538 BATF 0.003946406 3.94 4.79 1.8 BrAr:LOC27319_at LOC27319 BHLHE22 0.000832399 2.72 3.13 1.33 BrAr:LOC51411_at LOC51411 BIN2 0.001478985 5.15 6.3 2.22 BrAr:LOC653_at LOC653 BMP5 0.003429408 2.26 2.64 1.3 BrAr:LOC22903_at LOC22903 BTBD3 0.004900034 5.7 5.01 0.62 BrAr:LOC686_at LOC686 BTD 0.000105266 4.7 3.99 0.61 BrAr:LOC53838_at LOC53838 C11ORF24 0.003520261 4.97 5.3 1.26 BrAr:LOC399949_at LOC399949 C11ORF88  7.2489E−06 2.12 2.52 1.32 BrAr:LOC143678_at LOC143678 C11ORF94 2.49371E−05 1.99 2.35 1.28 BrAr:LOC79415_at LOC79415 C17ORF62 0.006116147 5.76 6.21 1.37 BrAr:LOC374872_at LOC374872 C19ORF35 0.009042774 3.6 3.93 1.26 BrAr:LOC126567_at LOC126567 C2CD4C 0.000755252 2.93 3.36 1.34 BrAr:LOC27202_at LOC27202 C5AR2 0.00698718 3.44 3.79 1.27 BrAr:LOC63920_at LOC63920 C5ORF54 0.008739816 4.08 3.54 0.69 BrAr:LOC91768_at LOC91768 CABLES1 0.002940092 4.9 4.14 0.59 BrAr:LOC440068_at LOC440068 CARD17 0.004061575 2.66 3.06 1.32 BrAr:LOC117144_at LOC117144 CATSPER1 0.005573531 3.35 3.98 1.54 BrAr:LOC55013_at LOC55013 CCDC109B 0.009687793 6.15 6.92 1.7 BrAr:LOC256309_at LOC256309 CCDC110 0.006222969 2.57 1.9 0.63 BrAr:LOC28952_at LOC28952 CCDC22 8.79954E−05 4.24 4.7 1.37 BrAr:LOC342510_at LOC342510 CD300E 0.009277761 3.72 4.1 1.3 BrAr:LOC916_at LOC916 CD3E 0.005229998 4.67 6.1 2.7 BrAr:LOC924_at LOC924 CD7 0.000599999 3.22 3.68 1.37 BrAr:LOC3732_at LOC3732 CD82 0.007778158 3.14 3.65 1.43 BrAr:LOC997_at LOC997 CDC34 0.001777585 4.04 4.48 1.36 BrAr:LOC1084_at LOC1084 CEACAM3 0.00167501 3.74 4.07 1.26 BrAr:LOC145508_at LOC145508 CEP128 0.000595015 3.88 4.52 1.56 BrAr:LOC1675_at LOC1675 CFD 0.004220607 3.35 4.19 1.79 BrAr:LOC63924_at LOC63924 CIDEC 0.000915451 2.49 2.89 1.32 BrAr:LOC8483_at LOC8483 CILP 0.003154463 2.92 4.16 2.36 BrAr:LOC9976_at LOC9976 CLEC2B 0.000938528 7.17 8.14 1.95 BrAr:LOC339390_at LOC339390 CLEC4G 0.000637875 2.52 2.85 1.25 BrAr:LOC79827_at LOC79827 CLMP 0.002162595 3.58 4.55 1.97 BrAr:LOC23059_at LOC23059 CLUAP1 0.004273619 5.58 5.18 0.76 BrAr:LOC10229_at LOC10229 COQ7 0.009767632 6.08 5.58 0.71 BrAr:LOC1355_at LOC1355 COX15 0.001550291 6.25 5.85 0.76 BrAr:LOC1409_at LOC1409 CRYAA ∥ ? 0.009195632 2.83 3.32 1.41 BrAr:LOC64651_at LOC64651 CSRNP1 0.001153343 4.95 5.34 1.31 BrAr:LOC1521_at LOC1521 CTSW 0.001728422 3.73 4.57 1.79 BrAr:LOC1522_at LOC1522 CTSZ 0.007645829 7.64 8.38 1.67 BrAr:LOC9267_at LOC9267 CYTH1 0.004664342 5.12 5.62 1.41 BrAr:LOC27128_at LOC27128 CYTH4 0.007386637 3.49 3.94 1.37 BrAr:LOC153090_at LOC153090 DAB2IP 0.002227001 5.59 4.92 0.63 BrAr:LOC28988_at LOC28988 DBNL 0.002200102 5.51 5.93 1.34 BrAr:LOC84516_at LOC84516 DUNS 0.001890579 6.09 5.66 0.75 BrAr:LOC22898_at LOC22898 DENND3 0.001155438 3.77 4.32 1.46 BrAr:LOC27123_at LOC27123 DKK2 0.000782988 2.91 3.6 1.62 BrAr:LOC1741_at LOC1741 DLG3 0.001806326 5.95 5.4 0.68 BrAr:LOC131118_at LOC131118 DNAJC19 0.006866278 7.24 6.59 0.64 BrAr:LOC1796_at LOC1796 DOK1 0.002452713 3.71 4.11 1.33 BrAr:LOC9046_at LOC9046 DOK2 0.009504175 3.63 4.13 1.42 BrAr:LOC10589_at LOC10589 DRAP1 0.001830494 6.35 6.87 1.44 BrAr:LOC9666_at LOC9666 DZIP3 0.002893835 4.96 4.32 0.64 BrAr:LOC1874_at LOC1874 E2F4 0.005888969 5.01 5.34 1.26 BrAr:LOC144455_at LOC144455 E2F7 0.00060632 2.54 3.2 1.58 BrAr:LOC79180_at LOC79180 EFHD2 0.001533709 5.24 5.98 1.67 BrAr:LOC25975_at LOC25975 EGFL6 0.006225321 2.62 3.28 1.58 BrAr:LOC254102_at LOC254102 EHBP1L1 0.001083093 3.6 4.21 1.52 BrAr:LOC1964_at LOC1964 EIF1AX 0.007627306 7.33 6.88 0.73 BrAr:LOC1979_at LOC1979 EIF4EBP2 0.002832149 7.95 7.49 0.73 B rAr:LO C2000_at LOC2000 ELF4 0.009430975 6.83 7.3 1.39 BrAr:LOC2036_at LOC2036 EPB41L1 0.000854408 6.9 5.9 0.5 BrAr:LOC11160_at LOC11160 ERLIN2 0.002726397 5.12 4.61 0.7 BrAr:LOC79956_at LOC79956 ERMP1 0.003099694 6.44 5.84 0.66 BrAr:LOC2121_at LOC2121 EVC 0.003766926 3.36 3.7 1.27 BrAr:LOC2124_at LOC2124 EVI2B 0.008272345 6.7 7.65 1.93 BrAr:LOC150864_at LOC150864 FAM117B 0.000508571 5.61 4.94 0.63 BrAr:LOC642968_at LOC642968 FAM163B 0.000315427 2.4 2.73 1.26 BrAr:LOC54757_at LOC54757 FAM20A 0.008983202 4.16 4.9 1.68 BrAr:LOC84293_at LOC84293 FAM213A 0.009083801 8.7 8.03 0.63 BrAr:LOC84961_at LOC84961 FBXL20 0.001990936 5.33 4.92 0.75 BrAr:LOC26273_at LOC26273 FBXO3 0.005774007 5.24 4.72 0.7 BrAr:LOC26270_at LOC26270 FBXO6 0.004151206 2.91 3.44 1.44 BrAr:LOC115352_at LOC115352 FCRL3 0.008603096 3.18 3.77 1.51 BrAr:LOC121512_at LOC121512 FGD4 0.006220203 5.57 5.04 0.69 BrAr:LOC392490_at LOC392490 FLJ44635 0.005825881 2.91 3.26 1.27 BrAr:LOC2323_at LOC2323 FLT3LG 0.001059924 3.88 4.29 1.33 BrAr:LOC752_at LOC752 FMNL1 0.005673631 3.19 3.87 1.61 BrAr:LOC2444_at LOC2444 FRK 0.007354384 5.41 4.63 0.59 BrAr:LOC53827_at LOC53827 FXYD5 0.00949403 7.52 8.12 1.52 BrAr:LOC4616_at LOC4616 GADD45B 0.006110882 6.38 7.07 1.61 BrAr:LOC2585_at LOC2585 GALK2 0.002535719 5.6 5.06 0.69 BrAr:LOC79623_at LOC79623 GALNT14 0.007555669 7.43 6.42 0.49 BrAr:LOC8484_at LOC8484 GALR3 0.002225231 2.88 3.21 1.26 BrAr:LOC2634_at LOC2634 GBP2 0.00169654 9.1 9.68 1.5 BrAr:LOC115362_at LOC115362 GBPS 0.004448746 5.71 7.15 2.71 BrAr:LOC2662_at LOC2662 GDF10 9.97246E−05 2.18 2.53 1.27 BrAr:LOC8328_at LOC8328 GFI1B 0.000528856 2.71 3.07 1.29 BrAr:LOC84340_at LOC84340 GFM2 0.006257568 5.52 5.03 0.71 BrAr:LOC9945_at LOC9945 GFPT2 0.001612889 4.86 5.72 1.82 BrAr:LOC10804_at LOC10804 GJB6 0.009481221 2.13 3.03 1.87 BrAr:LOC26035_at LOC26035 GLCE 0.007331368 6.44 5.76 0.62 BrAr:LOC728310_at LOC728310 GOLGA6L7P 0.002663795 4.18 4.58 1.33 BrAr:LOC151306_at LOC151306 GPBAR1 0.001078179 3.82 4.3 1.4 BrAr:LOC2825_at LOC2825 GPR1 1.12776E−05 2.32 2.72 1.32 BrAr:LOC222487_at LOC222487 GPR97 0.006093072 3.3 3.77 1.39 BrAr:LOC3002_at LOC3002 GZMB 0.002027831 4.42 5.91 2.81 BrAr:LOC3037_at LOC3037 HAS2 0.00079141 2.97 3.64 1.6 BrAr:LOC25831_at LOC25831 HECTD1 0.004167883 6.92 6.43 0.71 BrAr:LOC8355_at LOC8355 HIST1H3G 0.002866252 3.41 4.12 1.64 BrAr:LOC84263_at LOC84263 HSDL2 0.006343005 6.57 6.02 0.68 BrAr:LOC84941_at LOC84941 HSH2D 0.005527177 3.85 4.31 1.37 BrAr:LOC147920_at LOC147920 IGFL2 0.001338112 2.98 3.74 1.69 BrAr:LOC9641_at LOC9641 IKBKE 0.006567351 3.51 3.96 1.37 BrAr:LOC3601_at LOC3601 IL15RA 0.006778476 5.15 5.78 1.55 BrAr:LOC3552_at LOC3552 IL1A 0.000381983 2.34 2.91 1.48 BrAr:LOC7850_at LOC7850 IL1R2 0.00913524 4.99 6.31 2.51 BrAr:LOC51194_at LOC51194 IPO11 ∥ IPO11- 0.001524954 6.28 5.73 0.68 LRRC70 BrAr:LOC3659_at LOC3659 IRF1 0.001881433 4.94 5.72 1.72 BrAr:LOC8471_at LOC8471 IRS4 0.00026598 2.09 2.6 1.43 BrAr:LOC150771_at LOC150771 ITPRIPL1 0.006231421 2.75 3.12 1.29 BrAr:LOC3744_at LOC3744 KCNA10 0.000801613 2.88 3.2 1.25 BrAr:LOC3742_at LOC3742 KCNA6 0.001284042 3.59 3.94 1.27 BrAr:LOC8514_at LOC8514 KCNAB2 0.008920942 3.34 3.72 1.3 BrAr:LOC3751_at LOC3751 KCND2 0.000823109 2.39 2.93 1.46 BrAr:LOC3783_at LOC3783 KCNN4 0.000453519 3.34 3.91 1.49 BrAr:LOC55196_at LOC55196 KIAA1551 0.000793589 7.13 7.87 1.67 BrAr:LOC80726_at LOC80726 KIAA1683 0.000217967 3.78 4.13 1.27 BrAr:LOC55083_at LOC55083 KIF26B 0.007631673 3.08 3.53 1.37 BrAr:LOC3833_at LOC3833 KIFC1 0.008302118 3.86 4.32 1.37 BrAr:LOC54800_at LOC54800 KLHL24 0.001808739 8.36 7.93 0.75 BrAr:LOC386677_at LOC386677 KRTAP10-1 0.007741563 4.54 4.93 1.31 BrAr:LOC386682_at LOC386682 KRTAP10-3 0.003161767 3.77 4.15 1.31 BrAr:LOC51520_at LOC51520 LARS 0.000220464 6.63 6.16 0.72 BrAr:LOC253558_at LOC253558 LCLAT1 0.008215165 6.8 6.3 0.71 BrAr:LOC100287902_at LOC100287902 LGALS8-AS1 0.006350303 2.37 2.7 1.25 BrAr:LOC23547_at LOC23547 LILRA4 0.00040177 2.8 3.21 1.32 BrAr:LOC10990_at LOC10990 LILRB5 0.006482713 3.59 4.05 1.37 BrAr:LOC55327_at LOC55327 LIN7C 0.003833811 7.5 7.04 0.72 BrAr:LOC54072_at LOC54072 LINC00158 0.00672404 2.28 2.74 1.37 BrAr:LOC79940_at LOC79940 L1NC00472 0.006488207 4.47 3.44 0.49 BrAr:LOC100134259_at LOC100134259 LINC01119 0.000625649 2.76 3.08 1.25 BrAr:LOC387787_at LOC387787 LIPT2 0.008893266 3.03 2.61 0.74 BrAr:LOC100288637_at LOC100288637 LOC100288637 0.005731863 5.25 5.69 1.35 BrAr:LOC10128_at LOC10128 LRPPRC 0.001065237 6.79 6.26 0.69 BrAr:LOC26231_at LOC26231 LRRC29 4.34623E−05 3.71 4.18 1.39 BrAr:LOC84967_at LOC84967 LSM10 0.001372205 4.75 5.27 1.43 BrAr:LOC4050_at LOC4050 LTB 0.005018671 4.3 5.02 1.64 BrAr:LOC4124_at LOC4124 MAN2A1 0.007495834 5.26 4.81 0.73 BrAr:LOC10299_at LOC10299 MARCH6 0.004816187 8.96 8.45 0.7 BrAr:LOC255374_at LOC255374 MBLAC1 0.003068993 4.44 3.83 0.66 BrAr:LOC284207_at LOC284207 METRNL 0.000642659 3.35 3.8 1.37 BrAr:LOC254013_at LOC254013 METTL20 0.000117399 4.43 3.69 0.6 BrAr:LOC4277_at LOC4277 MICB 0.000321554 3.49 3.96 1.38 BrAr:LOC54471_at LOC54471 MIEF1 0.000410552 4.92 4.51 0.75 BrAr:LOC60672_at LOC60672 MIIP 0.004931523 4.76 5.16 1.32 BrAr:LOC4314_at LOC4314 MIMP3 4.97409E−07 2.19 3.92 3.33 BrAr:LOC64112_at LOC64112 MOAP1 0.008394216 7.08 6.53 0.68 BrAr:LOC64398_at LOC64398 MPP5 0.006167145 6.7 6.24 0.73 BrAr:LOC64976_at LOC64976 MRPL40 0.007764465 8.23 7.77 0.73 BrAr:LOC23107_at LOC23107 MRPS27 0.001414269 5.83 5.31 0.7 BrAr:LOC343930_at LOC343930 MSGN1 0.000579512 2.74 3.07 1.26 BrAr:LOC4437_at LOC4437 MSH3 0.00389965 5.54 5.11 0.74 BrAr:LOC10232_at LOC10232 MSLN 0.008092046 2.27 2.6 1.26 BrAr:LOC4488_at LOC4488 MSX2 0.001329214 3.04 3.52 1.4 BrAr:LOC55149_at LOC55149 MTPAP 0.000627336 4.42 3.91 0.7 BrAr:LOC57509_at LOC57509 MTUS1 0.003060695 6.21 5.31 0.54 BrAr:LOC4588_at LOC4588 MUC6 0.004734191 3.43 3.78 1.27 BrAr:LOC4595_at LOC4595 MUTYH 0.000171 3.18 3.53 1.28 BrAr:LOC4542_at LOC4542 MYO1F 0.008571913 5.44 6.3 1.82 BrAr:LOC64005_at LOC64005 MYO1G 5.55979E−05 2.55 2.93 1.3 BrAr:LOC4650_at LOC4650 MYO9B 0.005096816 3.22 3.64 1.33 BrAr:LOC342977_at LOC342977 NANOS3 0.000396627 2.89 3.21 1.25 BrAr:LOC222236_at LOC222236 NAPEPLD 0.008927534 4.79 4.33 0.72 BrAr:LOC4781_at LOC4781 NFIB 0.008871165 7.31 6.39 0.53 BrAr:LOC4818_at LOC4818 NKG7 0.003622084 5.83 6.89 2.08 BrAr:LOC255743_at LOC255743 NPNT 0.00344628 5.63 4.2 0.37 BrAr:LOC120796_at LOC120796 OR56A1 0.000432027 3.72 4.1 1.3 BrAr:LOC23762_at LOC23762 OSBP2 0.009185113 3.02 3.36 1.27 BrAr:LOC150677_at LOC150677 OTOS 0.000614992 3.08 3.44 1.28 BrAr:LOC56288_at LOC56288 PARD3 0.005865917 5.38 4.97 0.75 BrAr:LOC80714_at LOC80714 PBX4 0.000760261 3.32 3.84 1.43 BrAr:LOC5179_at LOC5179 PENK 1.15397E−05 2.06 2.69 1.54 BrAr:LOC5193_at LOC5193 PEX12 0.002594105 4.79 4.3 0.71 BrAr:LOC5824_at LOC5824 PEX19 0.006368879 6.17 5.7 0.72 BrAr:LOC5292_at LOC5292 PIM1 0.007345148 4.82 5.67 1.8 BrAr:LOC5341_at LOC5341 PLEK 0.00929435 6.12 7.15 2.03 BrAr:LOC59338_at LOC59338 PLEKHAl 0.007269683 7.18 6.39 0.58 BrAr:LOC23207_at LOC23207 PLEKHM2 0.009858656 4.36 4.71 1.28 BrAr:LOC51177_at LOC51177 PLEKHO1 0.0074894 8.2 8.81 1.53 BrAr:LOC51090_at LOC51090 PLLP 0.00772165 4.78 3.58 0.44 BrAr:LOC196051_at LOC196051 PPAPDCIA 0.000201087 2.24 2.96 1.64 BrAr:LOC5522_at LOC5522 PPP2R2C 0.008008356 2.83 3.34 1.42 BrAr:LOC84106_at LOC84106 PRAM1 0.003485915 3.62 4.21 1.51 BrAr:LOC9051_at LOC9051 PSTPIP1 0.002985194 3.37 3.99 1.53 BrAr:LOC2185_at LOC2185 PTK2B 0.007119679 3.8 4.32 1.43 BrAr:LOC5792_at LOC5792 PTPRF 0.007560515 7.18 6.56 0.65 BrAr:LOC79037_at LOC79037 PVRIG 0.008669818 6.44 7.26 1.77 BrAr:LOC347148_at LOC347148 QRFP 0.002381775 2.72 3.11 1.31 BrAr:LOC9910_at LOC9910 RABGAP1L 0.001179112 6.91 7.65 1.67 BrAr:LOC5880_at LOC5880 RAC2 0.008956919 5.63 6.68 2.07 BrAr:LOC5900_at LOC5900 RALGDS 0.005206308 4.29 4.75 1.37 BrAr:LOC11030_at LOC11030 RBPMS 0.008856938 7.14 6.49 0.63 BrAr:LOC348093_at LOC348093 RBPMS2 0.004997179 4.52 3.52 0.5 BrAr:LOC5968_at LOC5968 REG1B 0.003701446 2.49 2.99 1.41 BrAr:LOC5068_at LOC5068 REG3A 0.000511408 2.53 2.96 1.35 BrAr:LOC220441_at LOC220441 RNF152 0.005124915 4.58 3.4 0.44 BrAr:LOC285533_at LOC285533 RNF175 0.004745303 2.36 2.85 1.41 BrAr:LOC6098_at LOC6098 ROS1 0.001421936 2.35 2.82 1.38 BrAr:LOC284751_at LOC284751 RP11-290F20.1 0.002153538 3.64 4.05 1.33 BrAr:LOC653712_at LOC653712 RP11-723O4.2 0.006747128 3.23 3.58 1.28 BrAr:LOC441239_at LOC441239 RP11-797H7.5 0.00892347 3.24 3.58 1.26 BrAr:LOC6146_at LOC6146 RPL22 0.000447423 8.65 8.05 0.66 BrAr:LOC23248_at LOC23248 RPRD2 0.000980072 6.24 5.68 0.68 BrAr:LOC219790_at LOC219790 RTKN2 6.04892E−06 2.03 2.45 1.33 BrAr:LOC388015_at LOC388015 RTL1 0.000195172 2.75 3.09 1.26 BrAr:LOC6282_at LOC6282 S100A11 0.009482935 9.26 9.77 1.42 BrAr:LOC25813_at LOC25813 SAMM50 0.001748454 6.05 5.51 0.69 BrAr:LOC64092_at LOC64092 SAMSN1 0.008819902 5.26 6.23 1.96 BrAr:LOC6303_at LOC6303 SAT1 0.002195688 9.38 9.93 1.47 BrAr:LOC9522_at LOC9522 SCAMPI 0.001160461 7.53 7.17 0.78 BrAr:LOC49855_at LOC49855 SCAPER 0.00740715 4.81 4.34 0.72 BrAr:LOC677681_at LOC677681 SCARNA20 0.003490289 2.35 2.77 1.33 BrAr:LOC7356_at LOC7356 SCGB1A1 0.008222088 2.48 3.09 1.53 BrAr:LOC26984_at LOC26984 SEC22A 0.007747092 4.57 4.14 0.74 BrAr:LOC94009_at LOC94009 SERHL 0.006002332 4.23 3.31 0.53 BrAr:LOC619189_at LOC619189 SERINC4 0.006726625 4.09 3.75 0.79 BrAr:LOC23616_at LOC23616 SH3BP1 0.000535136 3.71 4.25 1.45 BrAr:LOC6496_at LOC6496 SIX3 5.00022E−05 2.3 2.68 1.3 BrAr:LOC283652_at LOC283652 SLC24A5 0.008605602 5.26 4.56 0.61 BrAr:LOC5250_at LOC5250 SLC25A3 0.008268775 9.07 8.72 0.78 BrAr:LOC643664_at LOC643664 SLC35G6 0.001852751 3.07 3.42 1.28 BrAr:LOC91607_at LOC91607 SLFN11 0.009145132 5.63 6 1.29 BrAr:LOC4090_at LOC4090 SMAD5 0.001746237 6.1 5.48 0.65 BrAr:LOC677815_at LOC677815 SNORA34 0.002017953 4.59 5.21 1.53 BrAr:LOC677832_at LOC677832 SNORA53 0.006626719 3.18 3.52 1.27 BrAr:LOC11262_at LOC11262 SP140 0.009581919 3.73 4.88 2.23 BrAr:LOC100131390_at LOC100131390 SP9 0.001887466 3.92 4.25 1.26 BrAr:LOC64648_at LOC64648 SPANXD ∥ 5.13918E−05 2.56 2.94 1.3 SPANXE BrAr:LOC389763_at LOC389763 SPATA31D1 0.000603214 2.72 3.06 1.26 BrAr:LOC6688_at LOC6688 SPI1 0.009982697 4.17 4.64 1.38 BrAr:LOC503542_at LOC503542 SPRN 0.006440302 3.11 3.45 1.27 BrAr:LOC399833_at LOC399833 SPRNP1 0.000820016 2.66 3.02 1.28 B rAr:LO C6725 at LOC6725 SRMS 0.001157127 2.56 2.91 1.27 BrAr:LOC6754_at LOC6754 SSTR4 0.001481682 3.49 3.87 1.3 BrAr:LOC11037_at LOC11037 STON1 0.005887841 4.97 4.22 0.59 BrAr:LOC94121_at LOC94121 SYTL4 0.005600715 4.69 5.05 1.28 BrAr:LOC10579_at LOC10579 TACC2 0.007019696 4.72 3.99 0.6 BrAr:LOC117289_at LOC117289 TAGAP 0.003061103 3.99 4.87 1.84 BrAr:LOC259290_at LOC259290 TAS2R31 0.000896064 2.82 3.22 1.32 BrAr:LOC374403_at LOC374403 TBC1D10C 0.007740885 3.13 3.7 1.49 BrAr:LOC79718_at LOC79718 TBL1XR1 0.004717765 8.65 8.23 0.75 BrAr:LOC285343_at LOC285343 TCAIM 0.002451025 5.12 4.68 0.74 BrAr:LOC340543_at LOC340543 TCEAL5 0.008738975 2.25 2.77 1.44 BrAr:LOC6954_at LOC6954 TCP11 0.000500883 3.37 3.76 1.31 BrAr:LOC157695_at LOC157695 TDRP 0.003793627 5.76 4.9 0.55 BrAr:LOC79896_at LOC79896 THNSL1 0.005125473 3.74 3.3 0.74 BrAr:LOC10245_at LOC10245 TIMM17B 0.008928311 2.88 3.26 1.3 BrAr:LOC9414_at LOC9414 TJP2 0.00524848 5.99 5.41 0.67 BrAr:LOC8277_at LOC8277 TKTL1 4.21036E−05 2.24 2.79 1.47 BrAr:LOC284186_at LOC284186 TMEM105 0.003550476 2.79 3.12 1.25 BrAr:LOC84216_at LOC84216 TMEM117 0.005294472 3.45 3.83 1.3 BrAr:LOC54972_at LOC54972 TMEM132A 0.007470194 3.92 4.28 1.29 BrAr:LOC147744_at LOC147744 TMEM190 0.00321492 3.5 3.83 1.26 BrAr:LOC100131211_at LOC100131211 TMEM194B 0.001358748 4.93 4.56 0.77 BrAr:LOC256130_at LOC256130 TMEM196 0.000704047 2.16 2.51 1.27 BrAr:LOC255043_at LOC255043 TMEM86B 0.007769635 2.89 3.28 1.31 BrAr:LOC7126_at LOC7126 INFAIP1 0.009595017 6.07 5.64 0.74 BrAr:LOC9804_at LOC9804 TOMM20 0.001452667 8.39 7.9 0.71 BrAr:LOC127262_at LOC127262 TPRG1L 0.009328823 6.53 6.2 0.8 BrAr:LOC58485_at LOC58485 TRAPPC1 0.003857304 7.98 8.34 1.29 BrAr:LOC10024_at LOC10024 TROAP 0.003342892 3.08 3.41 1.26 BrAr:LOC83707_at LOC83707 TRPT1 0.005403522 5.51 5.93 1.33 BrAr:LOC26526_at LOC26526 TSPAN16 0.007917814 2.54 2.87 1.26 BrAr:LOC23331_at LOC23331 TTC28 0.001645396 5.86 5.08 0.58 BrAr:LOC23548_at LOC23548 TTC33 0.002813375 4.32 3.87 0.73 BrAr:LOC117581_at LOC117581 TWIST2 0.000970578 3.8 4.27 1.38 BrAr:LOC84203_at LOC84203 TXNDC2 5.21975E−07 3.54 4.2 1.59 BrAr:LOC84747_at LOC84747 UNC119B 0.006490817 6.96 6.26 0.62 BrAr:LOC7381_at LOC7381 UQCRB 0.005477408 6.42 5.91 0.7 BrAr:LOC9958_at LOC9958 USP15 0.002632883 6.32 6.79 1.39 BrAr:LOC54532_at LOC54532 USP53 0.003345289 4.91 4.48 0.74 BrAr:LOC9217_at LOC9217 VAPB 0.003742321 6.89 6.49 0.76 BrAr:LOC7408_at LOC7408 VASP 0.0085207 4.19 4.86 1.59 BrAr:LOC7454_at LOC7454 WAS 0.002617183 4.38 5.06 1.61 BrAr:LOC8976_at LOC8976 WASL 0.005786824 5.95 5.5 0.73 BrAr:LOC81029_at LOC81029 WNT5B 0.000381404 2.8 3.17 1.29 BrAr:LOC25937_at LOC25937 WWTR1 0.008239544 9.07 8.56 0.7 BrAr:LOC7535_at LOC7535 ZAP70 0.003799558 3.27 3.63 1.28 BrAr:LOC22882_at LOC22882 ZHX2 0.002402316 9.6 9.06 0.68 BrAr:LOC7586_at LOC7586 ZKSCAN1 0.003865802 6.02 5.57 0.73 BrAr:LOC9202_at LOC9202 ZMYM4 0.008490749 4.95 4.6 0.78 BrAr:LOC94039_at LOC94039 ZNF101 0.003583557 4.67 5.4 1.66 BrAr:LOC7559_at LOC7559 ZNF12 0.003675848 7.13 6.78 0.78 BrAr:LOC7762_at LOC7762 ZNF215 0.009488907 2.82 3.22 1.32 BrAr:LOC339324_at LOC339324 ZNF260 0.009438142 5.44 5.02 0.75 BrAr:LOC84330_at LOC84330 ZNF414 1.51102E−05 2.9 3.31 1.33 BrAr:LOC58499_at LOC58499 ZNF462 0.000404504 6.85 5.89 0.52 BrAr:LOC84450_at LOC84450 ZNF512 0.00966092 5.28 4.92 0.78 BrAr:LOC619279_at LOC619279 ZNF704 0.007056823 3.51 2.87 0.64 BrAr:LOC163049_at LOC163049 ZNF791 0.008235588 5.85 5.42 0.74 BrAr:LOC84133_at LOC84133 ZNRF3 0.008712389 3.28 2.71 0.68 BrAr:LOC90204_at LOC90204 ZSWIM1 0.00049795 2.54 2.87 1.26

TABLE 6B Normalization of select genes presented in Table 6A relative to the mean of all values measured at baseline. RMA intensity Expression relative to Categorization value at Baseline Mean of all values at Baseline of response MICB NKG7 PVRIG SPI1 CLEC2B MICB NKG7 PVRIG SPI1 CLEC2B ≥20% decrease 3.66 9.01 8.56 4.62 8.24 0.96 6.86 3.64 1.18 1.62 ≥20% decrease 3.27 5.60 6.99 4.53 8.05 0.73 0.65 1.23 1.11 1.42 ≥20% decrease 3.50 5.21 6.80 3.71 7.51 0.87 0.49 1.08 0.63 0.97 ≥20% decrease 4.38 7.17 6.16 4.86 8.41 1.59 1.92 0.69 1.39 1.82 ≥20% decrease 4.15 6.29 7.50 3.91 9.45 1.35 1.04 1.74 0.72 3.75 ≥20% decrease 4.08 7.84 7.40 5.37 8.76 1.29 3.04 1.63 1.98 2.32 ≥20% decrease 3.93 5.77 7.85 4.67 8.38 1.16 0.73 2.23 1.22 1.78 ≥20% decrease 4.42 8.48 8.27 5.01 7.91 1.63 4.72 2.98 1.54 1.29 ≥20% decrease 4.33 5.89 6.31 5.18 9.40 1.53 0.78 0.77 1.74 3.63 ≥20% decrease 4.31 7.32 7.28 4.76 8.87 1.52 2.11 1.50 1.30 2.51 ≥20% decrease 4.21 7.26 7.97 5.41 8.06 1.41 2.04 2.43 2.04 1.43 ≥20% decrease 3.99 7.32 6.73 4.61 7.75 1.22 2.11 1.03 1.17 1.15 ≥20% decrease 3.96 6.74 6.55 4.94 7.86 1.18 1.41 0.91 1.47 1.24 <20% decrease 3.52 5.54 6.09 4.16 8.65 0.87 0.62 0.66 0.85 2.15 <20% decrease 3.94 5.08 6.66 4.85 9.68 1.17 0.45 0.97 1.39 4.39 <20% decrease 3.86 6.89 8.63 4.57 8.40 1.10 1.57 3.82 1.14 1.80 <20% decrease 3.80 4.86 6.45 4.57 6.22 1.06 0.39 0.84 1.13 0.40 <20% decrease 2.97 7.26 6.49 3.51 6.22 0.60 2.04 0.87 0.55 0.40 <20% decrease 3.60 6.54 6.84 4.58 8.96 0.93 1.23 1.11 1.15 2.67 <20% decrease 3.77 5.33 6.41 4.87 6.49 1.04 0.53 0.82 1.40 0.48 <20% decrease 3.72 6.02 6.60 4.15 6.20 1.01 0.86 0.93 0.85 0.39 <20% decrease 3.41 4.50 5.27 4.39 6.83 0.81 0.30 0.37 1.00 0.61 <20% decrease 3.20 4.50 6.13 3.87 6.70 0.70 0.30 0.68 0.70 0.56 <20% decrease 3.82 6.61 7.09 4.27 6.01 1.08 1.29 1.32 0.92 0.34 <20% decrease 3.90 7.03 6.91 4.04 6.47 1.14 1.74 1.16 0.79 0.48 <20% decrease 3.86 8.18 7.40 5.11 8.06 1.11 3.86 1.64 1.65 1.42 <20% decrease 3.38 4.78 5.74 4.25 7.64 0.79 0.36 0.52 0.91 1.07 <20% decrease 3.21 4.32 5.78 3.76 6.81 0.71 0.26 0.53 0.65 0.60 <20% decrease 3.23 4.90 6.10 3.96 4.81 0.72 0.40 0.66 0.75 0.15 <20% decrease 3.35 4.63 5.75 3.73 6.53 0.78 0.33 0.52 0.64 0.49 <20% decrease 3.95 7.92 7.31 4.45 7.03 1.18 3.22 1.53 1.05 0.70 <20% decrease 3.82 7.04 6.57 4.68 7.51 1.07 1.75 0.92 1.23 0.97 <20% decrease 3.69 5.30 6.18 3.66 7.68 0.98 0.52 0.70 0.60 1.10 <20% decrease 3.61 4.64 5.04 3.93 7.73 0.93 0.33 0.32 0.73 1.14 <20% decrease 3.28 4.57 6.23 4.08 7.18 0.74 0.32 0.72 0.81 0.77 <20% decrease 3.03 5.97 6.18 3.77 7.09 0.62 0.83 0.70 0.65 0.73 <20% decrease 3.74 8.02 6.95 4.51 7.96 1.02 3.43 1.20 1.09 1.33 <20% decrease 3.70 6.66 7.10 4.21 7.78 0.99 1.34 1.32 0.89 1.18 <20% decrease 3.46 4.28 6.10 3.64 5.38 0.84 0.26 0.66 0.60 0.22 <20% decrease 3.68 5.79 6.64 5.67 8.13 0.98 0.74 0.96 2.44 1.50 <20% decrease 3.74 5.25 6.65 4.11 7.35 1.02 0.50 0.97 0.83 0.88 <20% decrease 4.21 6.09 6.19 3.56 9.35 1.41 0.90 0.71 0.57 3.48 <20% decrease 3.92 5.12 5.93 4.21 8.16 1.15 0.46 0.59 0.89 1.53 <20% decrease 3.70 8.71 7.66 4.33 7.47 0.99 5.55 1.96 0.97 0.95 <20% decrease 3.80 6.52 6.39 4.31 6.95 1.06 1.22 0.81 0.95 0.66 <20% decrease 3.37 5.00 6.43 3.60 6.07 0.79 0.42 0.83 0.58 0.36 <20% decrease 4.18 8.19 7.50 5.31 7.32 1.38 3.87 1.75 1.91 0.86 <20% decrease 3.37 5.57 5.46 4.13 8.18 0.79 0.63 0.43 0.84 1.55 <20% decrease 3.43 5.86 6.98 4.78 7.87 0.82 0.77 1.22 1.32 1.25 <20% decrease 3.88 8.44 8.10 5.15 8.14 1.13 4.61 2.66 1.70 1.51 <20% decrease 3.55 6.40 6.12 4.12 7.70 0.89 1.12 0.67 0.83 1.12 <20% decrease 3.28 5.88 6.11 4.37 7.42 0.74 0.78 0.67 0.99 0.92 <20% decrease 4.10 7.58 7.09 4.51 7.41 1.31 2.54 1.32 1.10 0.91 <20% decrease 3.59 5.26 6.57 3.92 6.42 0.92 0.51 0.92 0.72 0.46 <20% decrease 3.49 6.97 6.36 4.20 6.34 0.86 1.66 0.79 0.88 0.43 <20% decrease 3.61 5.32 6.31 3.99 7.62 0.93 0.53 0.77 0.76 1.05 Mean RMA, 3.71 6.24 6.69 4.38 7.55 all Patients Mean RMA, 4.01 6.92 7.26 4.74 8.36 Responders Fold-difference 1.23 1.60 1.48 1.28 1.76 in Mean values

TABLE 7A Genes From an Analysis of Tumor Biopsies With >1.2-fold or <0.8-fold DifferencesBetween Treatment Groups Before and After Treatment. P value for No Response v. Response Response: Response: No response: HUGO v. No Mean RMA Mean RMA Fold Probeset ENTREZ Gene Response value value difference (BrainArray v.10) Gene ID Symbol at C2D8 at C2D8 at C2D8 at C2D8 BrAr:LOC225_at LOC225 ABCD2 0.0012467 2.23 2.71 1.39 BrAr:LOC171586_at LOC171586 ABHD3 0.000906661 3.82 4.6 1.72 BrAr:LOC10006_at LOC10006 ABI1 0.003228742 7.56 7.88 1.25 BrAr:LOC100287036_at LOC100287036 AC137932.6 0.000569795 3.23 3.69 1.37 BrAr:LOC9744_at LOC9744 ACAP1 0.002971479 3.7 4.34 1.56 BrAr:LOC38_at LOC38 ACAT1 0.005640416 9.96 9.16 0.57 BrAr:LOC100_at LOC100 ADA 0.006118173 4.22 4.84 1.53 BrAr:LOC10863_at LOC10863 ADAM28 0.006146653 6 6.78 1.71 BrAr:LOC101_at LOC101 ADAM8 0.002707153 3.74 4.19 1.37 BrAr:LOC115_at LOC115 ADCY9 0.001524858 5.91 5.29 0.65 BrAr:LOC140_at LOC140 ADORA3 0.001167454 5.65 6.72 2.1 BrAr:LOC10939_at LOC10939 AFG3L2 0.00101786 6.21 5.54 0.63 BrAr:LOC116987_at LOC116987 AGAP1 0.009065365 5.18 4.76 0.75 BrAr:LOC177_at LOC177 AGER 0.002217024 3 3.36 1.29 BrAr:LOC192670_at LOC192670 AGO4 0.001209203 4.44 4.99 1.47 BrAr:LOC23287_at LOC23287 AGTPBP1 0.007729579 6.26 6.85 1.51 BrAr:LOC199_at LOC199 AIF1 0.003692163 8.56 9.3 1.67 BrAr:LOC9447_at LOC9447 AIM2 0.001621524 5.17 6.99 3.54 BrAr:LOC80709_at LOC80709 AKNA 0.001609129 3.21 3.8 1.51 BrAr:LOC1645_at LOC1645 AKR1C1 0.00526145 7.78 5.96 0.28 BrAr:LOC1646_at LOC1646 AKR1C2 0.002437391 6.33 4.63 0.31 BrAr:LOC130540_at LOC130540 ALS2CR12 7.7349E−05 3.04 3.73 1.61 BrAr:LOC154796_at LOC154796 AMOT 0.005299115 4.58 3.65 0.53 BrAr:LOC149992_at LOC149992 ANKRD30BP2 0.000727269 2.94 3.41 1.38 BrAr:LOC84250_at LOC84250 ANKRD32 0.000742431 5.74 6.4 1.58 BrAr:LOC57101_at LOC57101 ANO2 0.000400645 2.61 3.32 1.63 BrAr:LOC162_at LOC162 AP1B1 0.000507082 5.67 6.06 1.31 BrAr:LOC8905_at LOC8905 AP1S2 0.002796838 8.02 8.71 1.62 BrAr:LOC10717_at LOC10717 AP4B1 0.006391273 4.67 5.07 1.32 BrAr:LOC60489_at LOC60489 APOBEC3G 0.005710224 6.08 7.13 2.06 BrAr:LOC164668_at LOC164668 APOBEC3H 0.000140365 3.56 3.96 1.32 BrAr:LOC139322_at LOC139322 APOOL 0.000353552 8.31 7.81 0.71 BrAr:LOC351_at LOC351 APP 0.000185526 10.48 9.93 0.68 BrAr:LOC55843_at LOC55843 ARHGAP15 0.00219141 6.55 7.36 1.75 BrAr:LOC9938_at LOC9938 ARHGAP25 0.001914689 6.29 7.25 1.94 BrAr:LOC257106_at LOC257106 ARHGAP30 0.001105979 4.58 5.65 2.11 BrAr:LOC393_at LOC393 ARHGAP4 0.005535493 4.57 5.12 1.46 BrAr:LOC394_at LOC394 ARHGAP5 0.005400379 5.57 5.05 0.7 BrAr:LOC64333_at LOC64333 ARHGAP9 0.000273055 4.02 4.95 1.9 BrAr:LOC7984_at LOC7984 ARHGEF5 1.40777E−06 7.18 5.88 0.41 BrAr:LOC10865_at LOC10865 ARID5A 0.000149652 4.83 5.26 1.34 BrAr:LOC115761_at LOC115761 ARL11 1.2E−05 2.99 3.59 1.51 BrAr:LOC142686_at LOC142686 ASB14 0.008551171 4.02 4.36 1.27 BrAr:LOC51008_at LOC51008 ASCC1 0.002223687 6.69 6.15 0.69 BrAr:LOC430_at LOC430 ASCL2 0.001842603 5.34 5.89 1.47 BrAr:LOC445_at LOC445 ASS1 0.004568605 6.87 5.75 0.46 BrAr:LOC476_at LOC476 ATP1A1 0.009247333 11.16 10.72 0.74 BrAr:LOC481_at LOC481 ATP1B1 0.003199982 10.54 9.46 0.47 BrAr:LOC489_at LOC489 ATP2A3 0.001027403 3.89 4.49 1.52 BrAr:LOC506_at LOC506 ATP5B 0.008087795 10.21 9.58 0.65 BrAr:LOC79895_at LOC79895 ATP8B4 0.006027013 4.43 5.14 1.64 BrAr:LOC10409_at LOC10409 BASP1 0.005104092 8.35 9.38 2.04 BrAr:LOC10538_at LOC10538 BATF 6.5602E−05 4.25 5.45 2.28 BrAr:LOC11177_at LOC11177 BAZ1A 0.008213807 7.05 7.59 1.45 BrAr:LOC64919_at LOC64919 BCLUB 0.000434645 3.28 4.55 2.41 BrAr:LOC23743_at LOC23743 BHMT2 0.001978113 7.44 5.77 0.31 BrAr:LOC80114_at LOC80114 BICC1 7.78561E−05 6.48 5.37 0.46 BrAr:LOC51411_at LOC51411 BIN2 0.000237264 5.55 6.93 2.6 BrAr:LOC90427_at LOC90427 BMF 0.000637395 4.19 4.71 1.43 BrAr:LOC55589_at LOC55589 BMP2K 0.003980083 5.71 6.19 1.39 BrAr:LOC657_at LOC657 BMPR1A 7.43284E−05 6.38 5.36 0.49 BrAr:LOC663_at LOC663 BNIP2 0.006852177 7.21 7.62 1.33 BrAr:LOC283870_at LOC283870 BRICD5 0.00072577 4.42 4.87 1.37 BrAr:LOC339479_at LOC339479 BRINP3 0.000557819 2.41 2.77 1.28 BrAr:LOC7862_at LOC7862 BRPF1 0.000158804 3.31 3.75 1.36 BrAr:LOC84446_at LOC84446 BRSK1 0.00053125 3.7 4.29 1.5 BrAr:LOC695_at LOC695 BTK 0.001125632 2.66 3.24 1.5 BrAr:LOC121273_at LOC121273 C12ORF54 0.001468421 2.36 2.68 1.25 BrAr:LOC374467_at LOC144535 C12ORF55 0.003437712 2.32 2.65 1.25 BrAr:LOC283897_at C16ORF54 || ? 0.002932479 5.9 7.15 2.39 BrAr:LOC146556_at LOC146556 C16ORF89 0.006470581 4.38 4.95 1.49 BrAr:LOC79415_at LOC79415 C17ORF62 0.000899343 5.75 6.31 1.48 BrAr:LOC55337_at LOC55337 C19ORF66 0.007514937 5.39 5.83 1.36 BrAr:LOC128346_at LOC128346 C1ORF162 0.005672875 7.33 8.19 1.81 BrAr:LOC712_at LOC712 C1QA 0.002049065 5.86 6.83 1.96 BrAr:LOC713_at LOC713 C1QB 0.002586781 8.65 9.6 1.94 BrAr:LOC714_at LOC714 C1QC 0.001215013 7.71 8.66 1.93 BrAr:LOC26005_at LOC26005 C2CD3 1.55638E−05 3.24 3.74 1.41 BrAr:LOC718_at LOC718 C3 0.000524922 10.95 10.04 0.53 BrAr:LOC719_at LOC719 C3AR1 0.003525139 7.6 8.42 1.76 BrAr:LOC728_at LOC728 C5AR1 0.00481309 5.14 6.19 2.06 BrAr:LOC441108_at LOC441108 C5ORF56 3.09721E−05 3.4 4.05 1.57 BrAr:LOC133874_at LOC133874 C5ORF58 0.000865267 2.35 2.84 1.41 BrAr:LOC55262_at LOC55262 C7ORF43 7.45196E−05 3.56 4.01 1.37 BrAr:LOC51719_at LOC51719 CAB39 0.000708262 7.83 8.33 1.41 BrAr:LOC10486_at LOC10486 CAP2 0.007405167 7.26 6.23 0.49 BrAr:LOC65981_at LOC65981 CAPRIN2 0.000250068 4.39 5.09 1.63 BrAr:LOC114769_at LOC114769 CARD16 0.003494654 5.59 6.29 1.63 BrAr:LOC22900_at LOC22900 CARD8 0.000173925 5.86 6.55 1.62 BrAr:LOC64170_at LOC64170 CARD9 1.28773E−05 4.38 5.22 1.79 BrAr:LOC834_at LOC834 CASP1 0.002724277 6.61 7.39 1.72 BrAr:LOC863_at LOC863 CBFA2T3 0.005881378 2.48 2.95 1.39 BrAr:LOC865_at LOC865 CBFB 0.002240827 6.82 7.24 1.33 BrAr:LOC23468_at LOC23468 CBX5 0.00051764 8.65 8.1 0.69 BrAr:LOC343099_at LOC343099 CCDC18 0.00043805 4.4 4.92 1.44 BrAr:LOC8030_at LOC8030 CCDC6 0.008058159 7.77 7.32 0.73 BrAr:LOC440193_at LOC440193 CCDC88C 0.00674351 3.39 3.83 1.36 BrAr:LOC6368_at LOC6368 CCL23 0.000445198 2.36 2.94 1.49 BrAr:LOC6348_at LOC6348 CCL3 5.02254E−06 4.04 6.1 4.17 BrAr:LOC6351_at LOC6351 CCL4 0.000127014 8.12 9.35 2.34 BrAr:LOC6352_at LOC6352 CCL5 0.000764552 7.09 8.69 3.03 BrAr:LOC6355_at LOC6355 CCL8 8.16358E−05 4.01 5.79 3.43 BrAr:LOC83605_at LOC83605 CCM2 0.001340517 3.95 4.35 1.32 BrAr:LOC8900_at LOC8900 CCNA1 0.005854451 2.07 2.44 1.3 BrAr:LOC57018_at LOC57018 CCNL1 0.001128422 6.49 7.17 1.61 BrAr:LOC81669_at LOC81669 CCNL2 0.007592021 4.52 5.06 1.45 BrAr:LOC1230_at LOC1230 CCR1 0.001134927 5.62 6.83 2.33 BrAr:LOC1233_at LOC1233 CCR4 8.65555E−05 3.16 3.68 1.43 BrAr:LOC1234_at LOC1234 CCR5 0.001360935 4.72 6.05 2.53 BrAr:LOC9034_at LOC9034 CCRL2 0.001227378 4.29 5.39 2.14 BrAr:LOC10574_at LOC10574 CCT7 0.00800504 8.44 8.11 0.8 BrAr:LOC914_at LOC914 CD2 0.001090516 4.38 5.59 2.31 BrAr:LOC131450_at LOC131450 CD200R1 0.000220547 2.2 3.03 1.78 BrAr:LOC51744_at LOC51744 CD244 0.006585776 3.48 4.13 1.57 BrAr:LOC939_at LOC939 CD27 9.28841E−05 4.35 5.72 2.58 BrAr:LOC940_at LOC940 CD28 0.000390203 3.66 4.68 2.03 BrAr:LOC146722_at LOC146722 CD300LF 0.009992266 4.51 5.11 1.52 BrAr:LOC945_at LOC945 CD33 0.001827574 3.32 3.86 1.46 BrAr:LOC952_at LOC952 CD38 0.002437251 3.53 4.86 2.52 BrAr:LOC915_at LOC915 CD3D 0.001167151 6.07 7.73 3.15 BrAr:LOC916_at LOC916 CD3E 0.003022968 5.37 6.95 2.98 BrAr:LOC917_at LOC917 CD3G 0.008399115 5.89 7.19 2.48 BrAr:LOC923_at LOC923 CD6 4.99939E−05 2.56 2.89 1.26 BrAr:LOC968_at LOC968 CD68 0.004726071 8.27 9 1.65 BrAr:LOC969_at LOC969 CD69 0.000954582 4.05 5.6 2.93 BrAr:LOC924_at LOC924 CD7 0.000215612 3.3 3.8 1.42 BrAr:LOC8832_at LOC8832 CD84 0.008155386 6.07 7.05 1.98 BrAr:LOC942_at LOC942 CD86 0.007372391 4.84 5.69 1.8 BrAr:LOC925_at LOC925 CD8A 0.005143238 6.08 7.55 2.79 BrAr:LOC926_at LOC926 CD8B 7.12558E−05 3.05 4.51 2.75 BrAr:LOC10225_at LOC10225 CD96 0.002746719 3.96 4.92 1.94 BrAr:LOC23580_at LOC23580 CDC42EP4 0.005989914 6.31 5.89 0.74 BrAr:LOC56882_at LOC56882 CDC42SE1 0.001408363 6.9 7.46 1.47 BrAr:LOC50937_at LOC50937 CDON 0.004412943 4.45 3.52 0.53 BrAr:LOC1050_at LOC1050 CEBPA 0.005882136 5.39 6.24 1.8 BrAr:LOC1952_at LOC1952 CELSR2 0.002212027 5.97 5 0.51 BrAr:LOC145508_at LOC145508 CEP128 0.000205356 4.02 4.74 1.65 BrAr:LOC387119_at LOC387119 CEP85L 0.001263933 4.68 5.13 1.36 BrAr:LOC9023_at LOC9023 CH25H 0.001769097 2.83 3.42 1.51 BrAr:LOC26973_at LOC26973 CHORDCl 0.00935165 5.73 6.2 1.39 BrAr:LOC1145_at LOC1145 CHRNE 7.42355E−05 3.34 3.76 1.34 BrAr:LOC55501_at LOC55501 CHST12 4.32937E−06 3.47 4.04 1.49 BrAr:LOC11129_at LOC11129 CLASRP 0.005760158 4.46 5 1.45 BrAr:LOC10462_at LOC10462 CLEC10A 0.009296829 2.38 2.71 1.25 BrAr:LOC9976_at LOC9976 CLEC2B 0.000849039 7.21 8.2 1.99 BrAr:LOC29121_at LOC29121 CLEC2D 0.000154789 5.14 6.39 2.37 BrAr:LOC338339_at LOC338339 CLEC4D 0.005230637 2.75 3.49 1.67 BrAr:LOC64581_at LOC64581 CLEC7A 0.006805698 4.79 5.69 1.86 BrAr:LOC1195_at LOC1195 CLK1 0.006461537 7.4 7.94 1.45 BrAr:LOC23059_at LOC23059 CLUAP1 0.000805496 5.65 5.09 0.68 BrAr:LOC8418_at LOC8418 CMAHP 5.40572E−05 3.29 4.21 1.9 BrAr:LOC1240_at LOC1240 CMKLR1 0.00959365 4.89 5.54 1.57 BrAr:LOC129607_at LOC129607 CMPK2 0.002692027 3.44 4.06 1.54 BrAr:LOC146223_at LOC146223 CMTM4 0.001695882 5.54 4.84 0.62 BrAr:LOC112616_at LOC112616 CMTM7 2.28639E−05 4.83 5.81 1.98 BrAr:LOC25904_at LOC25904 CNOT10 0.005674705 4.75 5.1 1.27 BrAr:LOC28958_at LOC28958 COA3 0.004529243 7.61 6.85 0.59 BrAr:LOC22837_at LOC22837 COBLL1 0.004840016 5.83 5.01 0.57 BrAr:LOC27235_at LOC27235 COQ2 0.005978614 5.68 6.1 1.34 BrAr:LOC11151_at LOC11151 CORO1A 0.003258636 4.62 5.56 1.91 BrAr:LOC58487_at LOC58487 CREBZF 0.004478774 5.05 5.5 1.36 BrAr:LOC56253_at LOC56253 CRTAM 0.000220566 3.38 4.71 2.51 BrAr:LOC1410_at LOC1410 CRYAB 3.55009E−05 11.55 10.08 0.36 BrAr:LOC1441_at LOC1441 CSF3R 0.001115654 3.68 4.75 2.1 BrAr:LOC1445_at LOC1445 CSK 0.000228425 5.06 5.65 1.51 BrAr:LOC8530_at LOC8530 CST7 0.000603149 5.96 7.6 3.12 BrAr:LOC80169_at LOC80169 CTC1 0.000709519 3.06 3.4 1.27 BrAr:LOC1493_at LOC1493 CTLA4 0.003162168 3.62 4.58 1.93 BrAr:LOC1495_at LOC1495 CTNNA1 0.000660903 9.22 8.87 0.78 BrAr:LOC1508_at LOC1508 CTSB 0.005985191 9.97 10.5 1.45 BrAr:LOC1521_at LOC1521 CTSW 0.000149298 3.95 5.18 2.35 BrAr:LOC1522_at LOC1522 CTSZ 0.002000543 7.68 8.49 1.75 BrAr:LOC284340_at LOC284340 CXCL17 0.002487037 2.67 3.08 1.33 BrAr:LOC2833_at LOC2833 CXCR3 0.004868852 3.47 4.11 1.56 BrAr:LOC10663_at LOC10663 CXCR6 0.002518905 5.46 6.77 2.47 BrAr:LOC158830_at LOC158830 CXORF65 1.12446E−06 2.5 3.15 1.57 BrAr:LOC1540_at LOC1540 CYLD 0.002044721 4.74 5.22 1.39 BrAr:LOC9267_at LOC9267 CYTH1 0.000269468 5.23 5.89 1.58 BrAr:LOC27128_at LOC27128 CYTH4 0.000226778 3.49 4.11 1.54 BrAr:LOC9595_at LOC9595 CYTIP 0.00564827 4.85 5.99 2.19 BrAr:LOC1605_at LOC1605 DAG1 0.004336404 6.94 6.5 0.73 BrAr:LOC23604_at LOC23604 DAPK2 0.000168922 4.05 4.66 1.53 BrAr:LOC27071_at LOC27071 DAPP1 0.003238457 4.4 5.67 2.4 BrAr:LOC23576_at LOC23576 DDAH1 0.006783001 8.12 7.17 0.52 BrAr:LOC80821_at LOC80821 DDHD1 0.003836518 6.48 7.11 1.55 BrAr:LOC780_at LOC780 DDR1 0.002611921 5.78 4.89 0.54 BrAr:LOC91351_at LOC91351 DDX60L 0.001586639 5.53 6.33 1.73 BrAr:LOC50619_at LOC50619 DEF6 5.62458E−05 2.6 3.58 1.98 BrAr:LOC79961_at LOC79961 DENND2D 0.00608633 7.05 7.8 1.68 BrAr:LOC22898_at LOC22898 DENND3 0.008265605 3.77 4.26 1.4 BrAr:LOC1606_at LOC1606 DGKA 0.001067797 4.65 5.57 1.9 BrAr:LOC79132_at LOC79132 DHX58 5.94837E−05 3.22 3.57 1.27 BrAr:LOC1741_at LOC1741 DLG3 0.006616897 5.92 5.37 0.68 BrAr:LOC9231_at LOC9231 DLG5 0.004910244 6.33 5.88 0.73 BrAr:LOC23312_at LOC23312 DMXL2 0.005117223 5.51 6.18 1.59 BrAr:LOC1759_at LOC1759 DNM1 0.001682122 4.7 3.89 0.57 BrAr:LOC23268_at LOC23268 DNMBP 0.009281499 4.14 3.64 0.7 BrAr:LOC55619_at LOC55619 DOCK10 0.009910164 6.72 7.37 1.57 BrAr:LOC1794_at LOC1794 DOCK2 5.88991E−05 4.58 5.79 2.32 BrAr:LOC1796_at LOC1796 DOK1 0.000720179 3.64 4.11 1.39 BrAr:LOC9046_at LOC9046 DOK2 0.00010891 3.71 4.49 1.72 BrAr:LOC79930_at LOC79930 DOK3 0.005606473 4.09 4.76 1.6 BrAr:LOC25911_at LOC25911 DPCD 0.001635341 7.56 6.57 0.5 BrAr:LOC64174_at LOC64174 DPEP2 0.002593743 4.71 5.89 2.26 BrAr:LOC286148_at LOC286148 DPY19L4 0.008414163 7.02 6.59 0.74 BrAr:LOC1806_at LOC1806 DPYD 0.003034131 5.56 6.24 1.6 BrAr:LOC128338_at LOC128338 DRAM2 0.003935992 6.9 7.37 1.39 BrAr:LOC1829_at LOC1829 DSG2 0.00052769 6.38 4.67 0.31 BrAr:LOC401124_at LOC401124 DTHD1 0.004861568 2.98 3.48 1.41 BrAr:LOC1844_at LOC1844 DUSP2 0.000769069 2.79 3.14 1.28 BrAr:LOC1874_at LOC1874 E2F4 0.00176138 5.04 5.43 1.31 BrAr:LOC124454_at LOC124454 EARS2 0.003104123 4.38 4.02 0.78 BrAr:LOC80303_at LOC80303 EFHD1 0.007117336 4.98 3.79 0.44 BrAr:LOC79180_at LOC79180 EFHD2 0.007511702 5.54 6.15 1.52 BrAr:LOC1956_at LOC1956 EGFR 1.55289E−05 7.23 5.74 0.36 BrAr:LOC1959_at LOC1959 EGR2 0.003664288 3.56 3.97 1.33 BrAr:LOC254102_at LOC254102 EHBP1L1 0.000337433 3.59 4.32 1.66 BrAr:LOC1964_at LOC1964 EIF1AX 0.007746341 7.3 6.81 0.71 BrAr:LOC1979_at LOC1979 EIF4EBP2 0.002419451 7.98 7.5 0.71 BrAr:LOC79993_at LOC79993 ELOVL7 0.005737598 5.56 4.16 0.38 BrAr:LOC133418_at LOC133418 EMB 0.007214626 4.98 5.96 1.98 BrAr:LOC23065_at LOC23065 EMC1 0.004377503 6.71 6.21 0.71 BrAr:LOC9583_at LOC9583 ENTPD4 0.008166686 4.95 5.43 1.4 BrAr:LOC8320_at LOC8320 EOMES 0.000354844 3.2 4.36 2.24 BrAr:LOC2036_at LOC2036 EPB41L1 0.002126996 6.84 5.89 0.52 BrAr:LOC57669_at LOC57669 EPB41L5 0.002790213 4.08 3.46 0.65 BrAr:LOC4072_at LOC4072 EPCAM 5.45391E−05 7.61 4.64 0.13 BrAr:LOC54749_at LOC54749 EPDR1 0.00366304 6.23 5.43 0.58 BrAr:LOC94240_at LOC94240 EPSTI1 0.008201474 5.88 6.88 2 BrAr:LOC57488_at LOC57488 ESYT2 0.00758229 6.69 6.22 0.72 BrAr:LOC2123_at LOC2123 EVI2A 0.004048187 7.54 8.57 2.04 BrAr:LOC2124_at LOC2124 EVI2B 0.000797326 7.02 8.22 2.3 BrAr:LOC84923_at LOC84923 FAM104A 0.001116208 6.17 6.62 1.37 BrAr:LOC81558_at LOC81558 FAM117A 0.00957928 4.57 5.26 1.61 BrAr:LOC55007_at LOC55007 FAM118A 0.000350269 5.19 5.85 1.58 BrAr:LOC25854_at LOC25854 FAM149A 0.006327603 6.8 5.92 0.54 BrAr:LOC348378_at LOC348378 FAM159A 0.000325725 2.88 3.39 1.42 BrAr:LOC729830_at LOC729830 FAM160A1 0.002194721 5.53 4.24 0.41 BrAr:LOC10712_at LOC10712 FAM189B 0.001562034 7.32 6.76 0.68 BrAr:LOC100131897_at LOC100131897 FAM196B 1.61849E−06 3.72 4.27 1.46 BrAr:LOC51571_at LOC51571 FAM49B 0.007916123 7.05 7.72 1.58 BrAr:LOC374986_at LOC374986 FAM73A 0.009874403 6.63 6.13 0.7 BrAr:LOC286336_at LOC286336 FAM78A 0.000685947 3.66 4.43 1.71 BrAr:LOC286077_at LOC286077 FAM83H 0.006416324 4.84 3.99 0.55 BrAr:LOC10160_at LOC10160 FARP1 0.005161169 6.32 5.69 0.65 BrAr:LOC356_at LOC356 FASLG 0.004570784 3.26 3.97 1.63 BrAr:LOC2195_at LOC2195 FAT1 1.39101E−05 9.47 8.45 0.49 BrAr:LOC115290_at LOC115290 FBXO17 0.002681893 5.9 5 0.54 BrAr:LOC2204_at LOC2204 FCAR 0.008980063 2.74 3.22 1.4 BrAr:LOC2212_at LOC2212 FCGR2A 0.002857455 8.33 9.14 1.76 BrAr:LOC2217_at LOC2217 FCGRT 0.004742303 8.92 9.38 1.38 BrAr:LOC343413_at LOC343413 FCRL6 0.000105945 3.24 3.86 1.53 BrAr:LOC83706_at LOC83706 FERMT3 0.000152188 4.63 5.57 1.92 BrAr:LOC26127_at LOC26127 FGFR1OP2 8.43904E−06 7.91 8.54 1.54 BrAr:LOC81608_at LOC81608 FIP1L1 0.009198129 8.47 8.86 1.31 BrAr:LOC11328_at LOC11328 FKBP9 0.00768174 6.64 6.04 0.66 BrAr:LOC80308_at LOC80308 FLAD1 0.005616362 4.18 4.56 1.3 BrAr:LOC285150_at LOC285150 FLJ33534 0.005229915 3.31 3.67 1.29 BrAr:LOC752_at LOC752 FMNL1 0.00106439 3.26 4.1 1.78 BrAr:LOC64122_at LOC64122 FN3K 0.009685761 5.63 4.52 0.46 BrAr:LOC54874_at LOC54874 FNBP1L 0.001131939 7.43 6.37 0.48 BrAr:LOC2353_at LOC2353 FOS 0.001428641 2.71 3.51 1.74 BrAr:LOC2354_at LOC2354 FOSB 0.001418416 3.77 4.43 1.58 BrAr:LOC2290_at LOC2290 FOXG1 0.001807998 2.34 2.75 1.33 BrAr:LOC221937_at LOC221937 FOXK1 0.001511282 5.33 4.98 0.78 BrAr:LOC2444_at LOC2444 FRK 0.001867484 5.27 4.34 0.53 BrAr:LOC79068_at LOC79068 FTO 0.008108023 7.8 7.23 0.68 BrAr:LOC2517_at LOC2517 FUCA1 0.006928375 7.52 7.88 1.29 BrAr:LOC53827_at LOC53827 FXYD5 0.003668668 7.54 8.18 1.56 BrAr:LOC2533_at LOC2533 FYB 0.006370513 6.8 7.83 2.04 BrAr:LOC8321_at LOC8321 FZD1 0.000576837 7.17 6.39 0.58 BrAr:LOC2581_at LOC2581 GALC 0.005135891 5.7 6.18 1.39 BrAr:LOC79623_at LOC79623 GALNT14 0.007826728 7.35 5.79 0.34 BrAr:LOC2634_at LOC2634 GBP2 0.001383408 9.45 10.08 1.55 BrAr:LOC115362_at LOC115362 GBPS 0.000985486 6.53 8.25 3.3 BrAr:LOC25929_at LOC25929 GEMIN5 0.005334583 5.54 5.15 0.76 BrAr:LOC2672_at LOC2672 GFIl 0.000154364 4.06 4.84 1.71 BrAr:LOC2673_at LOC2673 GFPT1 0.00319937 7.1 6.69 0.75 BrAr:LOC170575_at LOC170575 GIMAP1 0.00022359 4.09 4.6 1.43 BrAr:LOC26157_at LOC26157 GIMAP2 0.005839193 6.59 7.43 1.79 BrAr:LOC55303_at LOC55303 GIMAP4 0.003717962 8.38 9.15 1.7 BrAr:LOC168537_at LOC168537 GIMAP7 0.003685418 7.91 8.87 1.94 BrAr:LOC256710_at LOC256710 GLIPR1L1 0.00202765 3.42 3.82 1.32 BrAr:LOC152007_at LOC152007 GLIPR2 0.002267318 6.52 7.44 1.89 BrAr:LOC169792_at LOC169792 GLIS3 0.009408735 4.64 4.11 0.69 BrAr:LOC9535_at LOC9535 GMFG 0.007629464 8.78 9.52 1.66 BrAr:LOC51291_at LOC51291 GMIP 4.20642E−05 3.43 4.19 1.69 BrAr:LOC2769_at LOC2769 GNA15 0.00246765 3.48 4.08 1.51 BrAr:LOC2770_at LOC2770 GNAI1 0.004652691 6.2 5.42 0.58 BrAr:LOC55970_at LOC55970 GNG12 0.002374064 7.64 6.99 0.63 BrAr:LOC57678_at LOC57678 GPAM 0.001956822 5.21 4.31 0.53 BrAr:LOC221914_at LOC221914 GPC2 0.009569549 4 4.43 1.35 BrAr:LOC166647_at LOC166647 GPR125 0.009449837 3.82 3.02 0.58 BrAr:LOC29909_at LOC29909 GPR171 0.00480987 4.98 6.28 2.46 BrAr:LOC84636_at LOC84636 GPR174 0.002524422 4.12 5.49 2.57 BrAr:LOC8477_at LOC8477 GPR65 0.00103869 4.16 5.16 2 BrAr:LOC27197_at LOC27197 GPR82 0.004696185 3.18 3.82 1.55 BrAr:LOC285513_at LOC285513 GPRIN3 0.009773641 5.1 5.79 1.62 BrAr:LOC63940_at LOC63940 GPSM3 0.001950781 5.47 6.41 1.92 BrAr:LOC2876_at LOC2876 GPX1 0.007974153 8.32 8.93 1.52 BrAr:LOC9402_at LOC9402 GRAP2 0.002136939 4.05 4.84 1.73 BrAr:LOC2885_at LOC2885 GRB2 0.001904691 7.67 8.16 1.41 BrAr:LOC23708_at LOC23708 GSPT2 0.006499379 4.36 4.69 1.25 BrAr:LOC2995_at LOC2995 GYPC 0.001913948 8.65 9.4 1.69 BrAr:LOC3001_at LOC3001 GZMA 0.003090567 8.03 9.39 2.57 BrAr:LOC3002_at LOC3002 GZMB 0.000184806 5.15 7.01 3.62 BrAr:LOC2999_at LOC2999 GZMH 0.004465152 6 7.53 2.88 BrAr:LOC3003_at LOC3003 GZMK 0.003988143 5.82 7.7 3.67 BrAr:LOC3004_at LOC3004 GZMM 0.000223193 3.17 3.62 1.37 BrAr:LOC3055_at LOC3055 HCK 0.002709241 5.07 5.88 1.75 BrAr:LOC3059_at LOC3059 HCLS1 0.008970756 6.33 7.25 1.9 BrAr:LOC10870_at LOC10870 HCST 0.001539626 5.38 6.37 1.99 BrAr:LOC3081_at LOC3081 HGD 0.001200099 7.79 5.93 0.28 BrAr:LOC8348_at LOC8348 HIST1H2BO 0.002966899 2.15 2.51 1.28 BrAr:LOC3133_at LOC3133 HLA-E 0.001498294 8.91 9.53 1.54 BrAr:LOC3141_at LOC3141 HLCS 0.001753289 4.39 3.92 0.72 BrAr:LOC6928_at LOC6928 HNF1B 0.001049148 6.53 5.01 0.35 BrAr:LOC3226_at LOC3226 HOXC10 0.002953491 6.98 5.74 0.42 BrAr:LOC9956_at LOC9956 HS3ST2 0.00370855 3.39 4.27 1.85 BrAr:LOC3291_at LOC3291 HSD11B2 0.008439525 4.81 3.67 0.45 BrAr:LOC3326_at LOC3326 HSP90AB1 0.002039686 10.96 10.49 0.72 BrAr:LOC3304_at LOC3304 HSPA1B 0.007974407 9.08 8.56 0.7 BrAr:LOC26353_at LOC26353 HSPB8 0.009342901 6.58 5.55 0.49 BrAr:LOC79663_at LOC79663 HSPBAP1 0.007672001 5.31 5.86 1.46 BrAr:LOC3329_at LOC3329 HSPD1 0.00697964 10.96 10.49 0.72 BrAr:LOC3385_at LOC3385 ICAM3 0.003007494 6.8 7.62 1.76 BrAr:LOC3400_at LOC3400 ID4 0.009458867 5.41 4.28 0.46 BrAr:LOC9592_at LOC9592 IER2 0.009528222 7.39 7.85 1.37 BrAr:LOC25900_at LOC25900 IFFO1 0.000639277 3.46 3.85 1.3 BrAr:LOC3458_at LOC3458 IFNG 1.86189E−05 2.71 4.13 2.68 BrAr:LOC3480_at LOC3480 IGF1R 0.00679354 5.74 5 0.6 BrAr:LOC10320_at LOC10320 IKZF1 0.008042369 5.26 6.15 1.86 BrAr:LOC22806_at LOC22806 IKZF3 0.008271122 4.95 6.37 2.68 BrAr:LOC3586_at LOC3586 IL10 0.002863799 2.59 2.97 1.3 BrAr:LOC3587_at LOC3587 IL10RA 0.001372236 3.37 4.05 1.6 BrAr:LOC3600_at LOC3600 IL15 0.001625719 3.14 3.76 1.55 BrAr:LOC3603_at LOC3603 IL16 0.000845357 4.44 5.31 1.82 BrAr:LOC3559_at LOC3559 IL2RA 0.001475194 4.13 5.29 2.23 BrAr:LOC3614_at LOC3614 IMPDH1 0.001505322 3.89 4.4 1.43 BrAr:LOC10207_at LOC10207 INADL 0.003879207 5.15 4.12 0.49 BrAr:LOC3631_at LOC3631 INPP4A 0.007352833 3.57 4.05 1.4 BrAr:LOC3635_at LOC3635 INPP5D 0.00112411 4.54 5.2 1.57 BrAr:LOC3640_at LOC3640 INSL3 0.004655003 2.66 3 1.26 BrAr:LOC3643_at LOC3643 INSR 0.006167598 7.17 6.21 0.51 BrAr:LOC79711_at LOC79711 IPO4 0.009040723 4.97 4.43 0.68 BrAr:LOC51135_at LOC51135 IRAK4 0.000346338 4.93 5.35 1.34 BrAr:LOC3659_at LOC3659 IRF1 0.002554721 5.44 6.26 1.75 BrAr:LOC3660_at LOC3660 IRF2 0.004250315 6.25 6.79 1.45 BrAr:LOC10379_at LOC10379 IRF9 0.002270511 5.73 6.24 1.43 BrAr:LOC79190_at LOC79190 IRX6 0.003746275 3.47 2.69 0.58 BrAr:LOC9636_at LOC9636 ISG15 0.003943514 7.87 8.6 1.66 BrAr:LOC3669_at LOC3669 ISG20 0.008015767 6.19 7.17 1.97 BrAr:LOC3676_at LOC3676 ITGA4 0.007770498 5.18 5.9 1.65 BrAr:LOC3695_at LOC3695 ITGB7 1.09194E−05 4.17 4.9 1.66 BrAr:LOC3696_at LOC3696 ITGB8 0.009774541 6.32 5.6 0.61 BrAr:LOC3702_at LOC3702 ITK 0.000614646 3.37 4.37 2 BrAr:LOC9767_at LOC9767 JADE3 0.004374851 5.16 4.67 0.71 BrAr:LOC3718_at LOC3718 JAK3 0.003488731 3.77 4.33 1.48 BrAr:LOC152789_at LOC152789 JAKMIP1 0.000267184 2.53 3.24 1.63 BrAr:LOC126306_at LOC126306 JSRP1 0.004431839 2.8 3.16 1.28 BrAr:LOC3726_at LOC3726 JUNB 0.000225013 5.03 5.55 1.44 BrAr:LOC8850_at LOC8850 KAT2B 0.007454606 5.58 6.19 1.52 BrAr:LOC84541_at LOC84541 KBTBD8 0.007562573 3.04 3.66 1.53 BrAr:LOC3738_at LOC3738 KCNA3 0.0058006 4.35 5.58 2.34 BrAr:LOC8514_at LOC8514 KCNAB2 4.1508E−05 3.38 3.99 1.53 BrAr:LOC3766_at LOC3766 KCNJ10 0.002550731 2.8 3.99 2.28 BrAr:LOC54442_at LOC54442 KCTD5 0.000154004 3.4 3.76 1.29 BrAr:LOC10765_at LOC10765 KDM5B 0.003578719 4.95 4.42 0.69 BrAr:LOC9834_at LOC9834 KIAA0125 0.009858424 3.39 4.13 1.66 BrAr:LOC80183_at LOC80183 KIAA0226L 0.008468237 3.63 4.29 1.58 BrAr:LOC55196_at LOC55196 KIAA1551 1.95908E−05 7.31 8.27 1.95 BrAr:LOC85379_at LOC85379 KIAA1671 0.003044192 6.99 6.18 0.57 BrAr:LOC8462_at LOC8462 KLF11 0.000172623 7.09 6.63 0.73 BrAr:LOC113730_at LOC113730 KLHDC7B 8.25644E−05 3.61 4.26 1.57 BrAr:LOC55175_at LOC55175 KLHL11 0.002335786 6.5 5.96 0.69 BrAr:LOC11275_at LOC11275 KLHL2 0.002161388 5.75 6.32 1.48 BrAr:LOC89857_at LOC89857 KLHL6 0.002656846 4.17 5.12 1.92 BrAr:LOC10219_at LOC10219 KLRG1 0.004918882 4.43 5.26 1.79 BrAr:LOC23633_at LOC23633 KPNA6 0.000721932 7.11 6.55 0.68 BrAr:LOC337985_at LOC337985 KRTAP20-3 0.000960059 2.94 3.28 1.26 BrAr:LOC3903_at LOC3903 LAIR1 0.002738539 4.9 5.73 1.78 BrAr:LOC55353_at LOC55353 LAPTM4B 0.001371449 8.58 7.76 0.57 BrAr:LOC51520_at LOC51520 LARS 0.009065446 6.6 6.23 0.78 BrAr:LOC7462_at LOC7462 LAT2 0.004658386 4.1 4.73 1.55 BrAr:LOC3932_at LOC3932 LCK 3.62704E−05 3.64 4.63 1.99 BrAr:LOC253558_at LOC253558 LCLAT1 0.000716258 6.84 6.14 0.61 BrAr:LOC3937_at LOC3937 LCP2 0.001771463 7.02 8.18 2.23 BrAr:LOC3965_at LOC3965 LGALS9 0.001147339 5.37 6.21 1.79 BrAr:LOC3981_at LOC3981 LIG4 0.001719114 2.71 3.09 1.3 BrAr:LOC10288_at LOC10288 LILRB2 0.009625864 6.8 7.9 2.15 BrAr:LOC11006_at LOC11006 LILRB4 0.001892547 4.12 5.17 2.08 BrAr:LOC10990_at LOC10990 LILRB5 0.007304563 3.53 4.12 1.5 BrAr:LOC80774_at LOC80774 LIMD2 0.001004901 7.19 8.24 2.08 BrAr:LOC55957_at LOC55957 LIN37 0.002341033 4.27 4.67 1.32 BrAr:LOC55327_at LOC55327 LIN7C 0.005757252 7.6 7.13 0.72 BrAr:LOC54072_at LOC54072 LINC00158 0.001209137 2.37 3.08 1.63 BrAr:LOC100507254_at LOC100507254 LINC01013 3.62726E−05 2.61 3.15 1.45 BrAr:LOC643418_at LOC643418 LIPN 0.002890607 2.09 2.49 1.33 BrAr:LOC100286925_at LOC100286925 LOC100286925 0.001015116 3.19 3.64 1.36 BrAr:LOC100289455_at LOC100289455 LOC100289455 0.001145861 3.29 3.65 1.29 BrAr:LOC100506748_at LOC100506748 LOC100506748 0.008166821 6.98 6.13 0.56 BrAr:LOC57121_at LOC57121 LPAR5 0.00875015 4.1 4.61 1.42 BrAr:LOC54947_at LOC54947 LPCAT2 0.006481437 5.75 6.44 1.62 BrAr:LOC9404_at LOC9404 LPXN 0.002413256 4.47 5.35 1.85 BrAr:LOC101060069_at LOC84859 LRCH3 0.006908809 4.77 5.16 1.31 BrAr:LOC57622_at LOC57622 LRFN1 0.006641146 2.64 2.98 1.27 BrAr:LOC4040_at LOC4040 LRP6 0.009500312 6.44 5.84 0.66 BrAr:LOC10128_at LOC10128 LRPPRC 0.001448129 6.78 6.25 0.69 BrAr:LOC126364_at LOC126364 LRRC25 0.007312481 4.46 4.93 1.39 BrAr:LOC57470_at LOC57470 LRRC47 3.37646E−05 8.67 8.07 0.66 BrAr:LOC84967_at LOC84967 LSM10 1.7086E−06 4.71 5.51 1.73 BrAr:LOC729862_at LSP1 || RP11- 7.43131E−05 7.01 7.59 1.49 14N7.2 || ? || LSP1P3 || ? || ? BrAr:LOC4056_at LOC4056 LTC4S 0.002016128 2.67 3.01 1.27 BrAr:LOC4063_at LOC4063 LY9 0.001081065 2.75 3.3 1.47 BrAr:LOC23643_at LOC23643 LY96 0.009105973 7.33 8.38 2.07 BrAr:LOC1130_at LOC1130 LYST 0.00025477 5.55 6.52 1.95 BrAr:LOC9935_at LOC9935 MAFB 0.002538157 5.98 6.96 1.97 BrAr:LOC114569_at LOC114569 MAL2 0.001540039 6.23 4.47 0.3 BrAr:LOC4125_at LOC4125 MAN2B1 0.000700622 6.33 7.04 1.64 BrAr:LOC389840_at LOC389840 MAP3K15 0.001025836 6.05 5.25 0.58 BrAr:LOC1326_at LOC1326 MAP3K8 0.000177401 3.32 4.02 1.63 BrAr:LOC11184_at LOC11184 MAP4K1 0.005700934 4.03 4.79 1.69 BrAr:LOC55016_at LOC55016 MARCH1 0.006442113 6.49 7.27 1.71 BrAr:LOC153562_at LOC153562 MARVELD2 0.003345363 5.43 4.06 0.39 BrAr:LOC64087_at LOC64087 MCCC2 0.001691149 7.47 6.66 0.57 BrAr:LOC4170_at LOC4170 MCL1 0.009694025 6.18 6.53 1.27 BrAr:LOC57192_at LOC57192 MCOLN1 0.002029101 5.95 6.44 1.41 BrAr:LOC4191_at LOC4191 MDH2 0.009556738 9.19 8.8 0.77 BrAr:LOC90390_at LOC90390 MED30 0.0097495 5.3 5.74 1.36 BrAr:LOC4210_at LOC4210 MEFV 0.004481657 2.61 3.18 1.48 BrAr:LOC4233_at LOC4233 MET 0.000481401 7.62 6.5 0.46 BrAr:LOC4242_at LOC4242 MFNG 0.000113115 4.18 4.64 1.38 BrAr:LOC388931_at LOC388931 MFSD2B 0.000281083 2.46 2.82 1.29 BrAr:LOC4257_at LOC4257 MGST1 0.004490845 9.01 7.75 0.42 BrAr:LOC4259_at LOC4259 MGST3 0.005680745 9.84 9.33 0.7 BrAr:LOC64780_at LOC64780 MICAL1 0.003883901 6.86 7.55 1.62 BrAr:LOC4277_at LOC4277 MICB 0.000795372 3.61 4.06 1.37 BrAr:LOC4281_at LOC4281 MID1 0.007325003 5.28 4.1 0.44 BrAr:LOC55320_at LOC55320 MIS18BP1 0.001818937 5.2 5.74 1.46 BrAr:LOC8569_at LOC8569 MKNK1 0.002977426 4.06 4.48 1.33 BrAr:LOC84451_at LOC84451 MLK4 0.002009063 6.2 4.96 0.42 BrAr:LOC79817_at LOC79817 MOB3B 0.002552689 5.23 4.24 0.5 BrAr:LOC51678_at LOC51678 MPP6 8.46017E−05 6.4 5.39 0.5 BrAr:LOC84689_at LOC84689 MS4A14 0.004152623 2.32 2.85 1.45 BrAr:LOC10943_at LOC10943 MSL3 3.96167E−05 3.91 4.31 1.32 BrAr:LOC4481_at LOC4481 MSR1 0.001295486 6.34 7.32 1.97 BrAr:LOC4498_at LOC4498 MT1JP 0.001398135 2.67 3.05 1.3 BrAr:LOC9219_at LOC9219 MTA2 0.008631439 3.83 4.17 1.26 BrAr:LOC22823_at LOC22823 MTF2 0.001229081 5.75 6.13 1.3 BrAr:LOC4600_at LOC4600 MX2 0.007586531 5.04 5.97 1.9 BrAr:LOC4641_at LOC4641 MYO1C 0.009584045 6.8 6.36 0.74 BrAr:LOC4542_at LOC4542 MYO1F 0.000979651 5.66 6.76 2.14 BrAr:LOC4644_at LOC4644 MYO5A 0.009021092 5.97 6.52 1.46 BrAr:LOC4650_at LOC4650 MYO9B 0.000964454 3.23 3.66 1.35 BrAr:LOC64859_at LOC64859 NABP1 0.001961157 6.56 7.54 1.97 BrAr:LOC65220_at LOC65220 NADK 0.004024885 4.32 4.76 1.36 BrAr:LOC51172_at LOC51172 NAGPA 0.001472846 4.11 4.45 1.27 BrAr:LOC222236_at LOC222236 NAPEPLD 0.008710095 4.78 4.28 0.71 BrAr:LOC4689_at LOC4689 NCF4 0.001234053 5.42 6.56 2.21 BrAr:LOC10787_at LOC10787 NCKAP1 0.000270123 8.41 7.77 0.64 BrAr:LOC23413_at LOC23413 NCS1 0.002517782 5.17 4.65 0.7 BrAr:LOC81565_at LOC81565 NDEL1 0.00044912 5.23 5.77 1.45 BrAr:LOC10397_at LOC10397 NDRG1 0.003695088 9.61 8.56 0.48 BrAr:LOC4753_at LOC4753 NELL2 0.008992092 4.3 5.12 1.76 BrAr:LOC4756_at LOC4756 NEO1 0.000155222 5.94 4.94 0.5 BrAr:LOC4763_at LOC4763 NF1 0.007244465 6.56 6.22 0.79 BrAr:LOC51199_at LOC51199 NIN 0.003683293 6.46 6.97 1.43 BrAr:LOC4818_at LOC4818 NKG7 0.000612039 6.42 7.9 2.8 BrAr:LOC4820_at LOC4820 NKTR 0.003766901 5.41 6.03 1.54 BrAr:LOC84166_at LOC84166 NLRC5 0.000330635 4.05 5.1 2.06 BrAr:LOC22861_at LOC22861 NLRP1 0.001909588 3.31 4 1.61 BrAr:LOC199713_at LOC199713 NLRP7 0.006716245 2.69 3.12 1.35 BrAr:LOC64127_at LOC64127 NOD2 0.002184673 2.63 3.19 1.47 BrAr:LOC55505_at LOC55505 NOP10 0.002678965 7.9 8.38 1.39 BrAr:LOC51491_at LOC51491 NOP16 0.008450601 6.59 6.01 0.67 BrAr:LOC80896_at LOC80896 NPL 0.000690308 5.67 6.94 2.41 BrAr:LOC29982_at LOC29982 NRBF2 0.000389607 6.36 7 1.56 BrAr:LOC375387_at LOC375387 NRROS 4.50837E−05 4.04 4.69 1.57 BrAr:LOC8439_at LOC8439 NSMAF 4.41796E−05 4.88 5.47 1.51 BrAr:LOC84628_at LOC84628 NTNG2 0.001660303 4.93 5.68 1.68 BrAr:LOC64710_at LOC64710 NUCKS1 0.005778725 8.86 8.48 0.77 BrAr:LOC10482_at LOC10482 NXF1 0.003244475 6.15 6.63 1.39 BrAr:LOC8638_at LOC8638 OASL 0.00362918 3.97 4.9 1.91 BrAr:LOC57489_at LOC57489 ODF2L 0.000757399 5.21 5.97 1.69 BrAr:LOC56957_at LOC56957 OTUD7B 0.009648978 4.8 4.4 0.76 BrAr:LOC92106_at LOC92106 OXNAD1 0.006226342 6.8 7.38 1.5 BrAr:LOC10606_at LOC10606 PAICS 0.000951329 8.18 7.46 0.61 BrAr:LOC10298_at LOC10298 PAK4 0.002616248 5.34 4.84 0.7 BrAr:LOC53354_at LOC53354 PANK1 0.003924872 7.01 5.72 0.41 BrAr:LOC167153_at LOC167153 PAPD4 0.007179274 5.69 6.17 1.39 BrAr:LOC56288_at LOC56288 PARD3 2.62632E−05 5.31 4.64 0.63 BrAr:LOC165631_at LOC165631 PARP15 0.000597574 2.41 3.18 1.71 BrAr:LOC79668_at LOC79668 PARP8 0.001033904 5.58 6.21 1.55 BrAr:LOC64098_at LOC64098 PARVG 3.02295E−07 4.78 5.58 1.74 BrAr:LOC197135_at LOC197135 PATL2 5.2694E−05 3.01 3.59 1.5 BrAr:LOC5076_at LOC5076 PAX2 0.003575147 4.67 3.83 0.56 BrAr:LOC80714_at LOC80714 PBX4 0.000750992 3.36 3.92 1.48 BrAr:LOC5096_at LOC5096 PCCB 0.006027555 5.97 5.3 0.63 BrAr:LOC56122_at LOC56122 PCDHB14 0.008482753 4.79 4.29 0.71 BrAr:LOC51449_at LOC51449 PCYOX1 0.000871122 7.51 6.8 0.61 BrAr:LOC80380_at LOC80380 PDCD1LG2 0.00249208 4.57 5.67 2.14 BrAr:LOC5140_at LOC5140 PDE3B 0.007301599 3.96 4.5 1.45 BrAr:LOC5142_at LOC5142 PDE4B 0.004457634 3.67 4.65 1.98 BrAr:LOC5148_at LOC5148 PDE6G 8.94693E−05 3.82 4.3 1.39 BrAr:LOC5152_at LOC5152 PDE9A 0.009685654 4.38 3.52 0.55 BrAr:LOC23089_at LOC23089 PEG10 0.004556464 4.76 3.48 0.41 BrAr:LOC5217_at LOC5217 PFN2 0.002114964 6.37 5.72 0.63 BrAr:LOC10857_at LOC10857 PGRMC1 0.006475701 9.61 9.02 0.66 BrAr:LOC9489_at LOC9489 PGS1 0.000369132 2.7 3.03 1.26 BrAr:LOC51131_at LOC51131 PHF11 0.00019631 5.68 6.25 1.48 BrAr:LOC84457_at LOC84457 PHYHIPL 0.009902214 4.94 3.93 0.5 BrAr:LOC8554_at LOC8554 PIAS1 0.002603807 6.34 6.76 1.33 BrAr:LOC5293_at LOC5293 PIK3CD 0.000699768 3.49 4.16 1.6 BrAr:LOC5294_at LOC5294 PIK3CG 0.00795533 5.21 6.01 1.74 BrAr:LOC23533_at LOC23533 PIK3R5 0.001975664 4.73 5.62 1.86 BrAr:LOC200576_at LOC200576 PIKFYVE 0.004438308 5.12 5.45 1.26 BrAr:LOC57095_at LOC57095 PITHD1 0.000620788 6.64 7.08 1.35 BrAr:LOC9033_at LOC9033 PKD2L1 7.38701E−05 3.89 4.98 2.13 BrAr:LOC8502_at LOC8502 PKP4 0.003912211 6.87 6.12 0.6 BrAr:LOC23659_at LOC23659 PLA2G15 0.000750241 4.57 4.9 1.26 BrAr:LOC26279_at LOC26279 PLA2G2D 0.007862004 3.33 4.02 1.61 BrAr:LOC5329_at LOC5329 PLAUR 0.002226155 5.31 6.56 2.38 BrAr:LOC5330_at LOC5330 PLCB2 0.001006462 2.75 3.19 1.35 BrAr:LOC23207_at LOC23207 PLEKHM2 0.004949319 4.19 4.56 1.29 BrAr:LOC51177_at LOC51177 PLEKHO1 0.003165857 8.41 9.1 1.61 BrAr:LOC80301_at LOC80301 PLEKHO2 0.005664231 6.43 7.1 1.59 BrAr:LOC10154_at LOC10154 PLXNC1 0.007188456 5.22 6.01 1.74 BrAr:LOC134359_at LOC134359 POC5 0.007629631 3.29 3.76 1.38 BrAr:LOC5425_at LOC5425 POLD2 0.005541595 6.74 6.09 0.64 BrAr:LOC10891_at LOC10891 PPARGC1A 0.002105868 6.16 4.32 0.28 BrAr:LOC8496_at LOC8496 PPFIBP1 0.005135014 6.39 5.74 0.64 BrAr:LOC132160_at LOC132160 PPM1M 0.000392111 4.9 5.67 1.71 BrAr:LOC26051_at LOC26051 PPP1R16B 0.006257791 3.87 4.45 1.5 BrAr:LOC170954_at LOC170954 PPP1R18 0.008008247 6.81 7.44 1.55 BrAr:LOC80316_at LOC80316 PPP1R2P9 1.60391E−05 2.09 2.43 1.27 BrAr:LOC55607_at LOC55607 PPP1R9A 0.001723064 5.18 3.96 0.43 BrAr:LOC55012_at LOC55012 PPP2R3C 0.000340239 6.33 7.07 1.66 BrAr:LOC5533_at LOC5533 PPP3CC 5.36619E−05 5.77 6.53 1.69 BrAr:LOC22870_at LOC22870 PPP6R1 0.000456639 6.15 6.72 1.49 BrAr:LOC57580_at LOC57580 PREX1 0.002348002 4.45 5.25 1.74 BrAr:LOC5551_at LOC5551 PRF1 0.000633167 4.5 5.7 2.3 BrAr:LOC5563_at LOC5563 PRKAA2 0.001193036 4.89 3.79 0.47 BrAr:LOC55119_at LOC55119 PRPF38B 0.002925833 6.13 6.47 1.27 BrAr:LOC260429_at LOC260429 PRSS33 0.00349208 2.29 2.9 1.52 BrAr:LOC9051_at LOC9051 PSTPIP1 4.32976E−05 3.41 4.3 1.86 BrAr:LOC5729_at LOC5729 PTGDR 0.000425807 2.38 2.81 1.34 BrAr:LOC5734_at LOC5734 PTGER4 0.000452488 4.44 5.24 1.74 BrAr:LOC5747_at LOC5747 PTK2 0.009028965 6.15 5.62 0.7 BrAr:LOC2185_at LOC2185 PTK2B 0.001623169 3.98 4.6 1.54 BrAr:LOC5771_at LOC5771 PTPN2 0.006868732 4.77 5.11 1.27 BrAr:LOC26191_at LOC26191 PTPN22 0.000805615 3.2 4.36 2.23 BrAr:LOC5774_at LOC5774 PTPN3 0.003383111 5.36 4.39 0.51 BrAr:LOC5777_at LOC5777 PTPN6 0.004965746 7.06 7.82 1.68 BrAr:LOC5778_at LOC5778 PTPN7 0.000995185 2.67 3.12 1.37 BrAr:LOC5788_at LOC5788 PTPRC 0.004701448 7.25 8.28 2.05 BrAr:LOC5790_at LOC5790 PTPRCAP 0.00029735 5.16 6.35 2.29 BrAr:LOC5792_at LOC5792 PTPRF 0.003117004 6.94 6.1 0.56 BrAr:LOC10744_at LOC10744 PTTG2 0.001807529 3.24 3.88 1.56 BrAr:LOC79037_at LOC79037 PVRIG 3.84156E−06 6.58 8.12 2.91 BrAr:LOC29108_at LOC29108 PYCARD 0.002026411 4.93 5.49 1.47 BrAr:LOC149628_at LOC149628 PYHIN1 0.000408398 4.51 5.61 2.14 BrAr:LOC5858_at LOC5858 PZP 0.000216348 3.19 4.09 1.86 BrAr:LOC26056_at LOC26056 RAB11FIP5 0.004593636 6.64 6.01 0.65 BrAr:LOC64284_at LOC64284 RAB17 0.006172675 7.39 5.88 0.35 BrAr:LOC5873_at LOC5873 RAB27A 0.000947493 6.09 6.84 1.68 BrAr:LOC10966_at LOC10966 RAB40B 0.002689147 7.65 6.79 0.55 BrAr:LOC9910_at LOC9910 RABGAP1L 0.000351958 6.99 7.85 1.81 BrAr:LOC64792_at LOC64792 RABL5 0.008308224 6.37 5.72 0.64 BrAr:LOC5880_at LOC5880 RAC2 0.001759421 6.1 7.38 2.42 BrAr:LOC5898_at LOC5898 RALA 0.003482967 7.81 8.31 1.41 BrAr:LOC5900_at LOC5900 RALGDS 5.09268E−06 4.17 4.94 1.71 BrAr:LOC5906_at LOC5906 RAP1A 0.005950215 9 9.4 1.32 BrAr:LOC5922_at LOC5922 RASA2 0.000504636 4.86 5.55 1.61 BrAr:LOC64926_at LOC64926 RASAL3 1.47228E−05 4.37 5.38 2.02 BrAr:LOC158158_at LOC158158 RASEF 0.002425894 5.87 4.62 0.42 BrAr:LOC10235_at LOC10235 RASGRP2 0.001039747 2.92 3.68 1.69 BrAr:LOC115727_at LOC115727 RASGRP4 0.007288134 3.02 3.73 1.64 BrAr:LOC11186_at LOC11186 RASSF1 0.001331649 3.94 4.32 1.31 BrAr:LOC83593_at LOC83593 RASSFS 0.001158992 4.31 5.22 1.87 BrAr:LOC166863_at LOC166863 RBM46 2.68055E−05 2.01 2.34 1.26 BrAr:LOC92241_at LOC92241 RCSD1 0.004611303 6.15 6.88 1.66 BrAr:LOC84957_at LOC84957 RELT 0.001573556 3.57 4.12 1.46 BrAr:LOC5973_at LOC5973 RENBP 0.000886528 2.38 2.75 1.29 BrAr:LOC266747_at LOC266747 RGL4 2.53719E−05 3.62 4.51 1.86 BrAr:LOC5996_at LOC5996 RGS1 0.000948891 4.25 5.94 3.24 BrAr:LOC10287_at LOC10287 RGS19 0.001238043 5.56 6.38 1.77 BrAr:LOC6007_at LOC6007 RHD 0.005520962 2.64 3.01 1.29 BrAr:LOC391_at LOC391 RHOG 0.001998079 5.78 6.39 1.53 BrAr:LOC85415_at LOC85415 RHPN2 0.004672418 6.05 4.84 0.43 BrAr:LOC11035_at LOC11035 RIPK3 0.000107974 2.49 2.82 1.26 BrAr:LOC79621_at LOC79621 RNASEH2B 0.000141017 5.85 6.52 1.6 BrAr:LOC7844_at LOC7844 RNF103 0.005704234 7.92 7.59 0.8 BrAr:LOC79589_at LOC79589 RNF128 0.006163854 6.73 5.53 0.43 BrAr:LOC115992_at LOC115992 RNF166 2.77285E−05 3.38 3.84 1.37 BrAr:LOC55599_at LOC55599 RNPC3 0.000969762 5.01 5.72 1.64 BrAr:LOC6195_at LOC6195 RPS6KA1 0.004714766 4.72 5.27 1.46 BrAr:LOC126638_at LOC126638 RPTN 0.002032449 1.89 2.23 1.26 BrAr:LOC91543_at LOC91543 RSAD2 0.008745842 5 6.13 2.18 BrAr:LOC154075_at LOC154075 SAMD3 0.005964418 3.88 4.66 1.71 BrAr:LOC219285_at LOC219285 SAMD9L 0.009330304 6.01 6.84 1.78 BrAr:LOC64092_at LOC64092 SAMSN1 0.000102994 5.55 6.97 2.68 BrAr:LOC54440_at LOC54440 SASH3 0.00085679 4.4 5.5 2.14 BrAr:LOC6303_at LOC6303 SAT1 0.000105426 9.5 10.19 1.62 BrAr:LOC132320_at LOC132320 SCLT1 0.003975976 5.67 6.13 1.37 BrAr:LOC9672_at LOC9672 SDC3 0.002541208 5.41 6.14 1.66 BrAr:LOC6385_at LOC6385 SDC4 0.000890801 8.12 6.99 0.46 BrAr:LOC10993_at LOC10993 SDS 0.006668039 4.91 5.91 2 BrAr:LOC81929_at LOC81929 SEH1L 0.001200528 6.64 6.12 0.7 BrAr:LOC6404_at LOC6404 SELPLG 1.27077E−05 3.91 4.81 1.87 BrAr:LOC57556_at LOC57556 SEMA6A 0.00940132 6.51 5.48 0.49 BrAr:LOC57337_at LOC57337 SENP7 0.003067422 4.38 4.86 1.39 BrAr:LOC1731_at LOC1731 SEPT1 0.000805403 3.89 4.82 1.91 BrAr:LOC653509_at LOC653509 SFTPA1 0.000239394 1.97 2.84 1.83 BrAr:LOC729238_at LOC729238 SFTPA2 0.001051605 2.33 3 1.59 BrAr:LOC6440_at LOC6440 SFTPC 0.000220741 2.41 2.85 1.35 BrAr:LOC166929_at LOC166929 SGMS2 0.001113196 4.98 4.48 0.71 BrAr:LOC4068_at LOC4068 SH2D1A 0.001779304 3.5 4.83 2.51 BrAr:LOC9047_at LOC9047 SH2D2A 0.000366782 2.79 3.45 1.58 BrAr:LOC23616_at LOC23616 SH3BP1 0.00025747 3.77 4.32 1.47 BrAr:LOC30011_at LOC30011 SH3KBP1 0.005587272 5.36 5.95 1.51 BrAr:LOC92799_at LOC92799 SHKBP1 1.06036E−05 4.07 4.56 1.4 BrAr:LOC27181_at LOC27181 SIGLEC8 0.004624284 3.14 3.92 1.72 BrAr:LOC27180_at LOC27180 SIGLEC9 0.008896966 3.48 4.24 1.69 BrAr:LOC6494_at LOC6494 SIPA1 0.00010627 4.4 4.97 1.49 BrAr:LOC55423_at LOC55423 SIRPG 0.001013982 3.77 5.02 2.37 BrAr:LOC27240_at LOC27240 SIT1 0.009541619 4.21 5.25 2.07 BrAr:LOC6503_at LOC6503 SLA 0.003691368 6.12 7.19 2.09 BrAr:LOC84174_at LOC84174 SLA2 4.01901E−05 3.44 4.37 1.9 BrAr:LOC114836_at LOC114836 SLAMF6 0.001206283 3.67 5.07 2.64 BrAr:LOC51296_at LOC51296 SLC15A3 0.008843878 5.28 5.94 1.57 BrAr:LOC10165_at LOC10165 SLC25A13 0.004725296 5.28 4.57 0.61 BrAr:LOC79085_at LOC79085 SLC25A23 0.00261534 6.15 5.24 0.53 BrAr:LOC11309_at LOC11309 SLCO2B1 0.004740526 4.67 5.2 1.44 BrAr:LOC342618_at LOC342618 SLFN14 0.000448431 2.11 2.5 1.31 BrAr:LOC60682_at LOC60682 SMAP1 0.008833996 5.88 6.2 1.25 BrAr:LOC64744_at LOC64744 SMAP2 0.000548688 6.58 7.54 1.95 BrAr:LOC333929_at LOC333929 SNAI3 6.31401E−05 3.45 3.86 1.33 BrAr:LOC684959_at LOC684959 SNORA25 0.000701791 5.18 6.92 3.35 BrAr:LOC677793_at LOC677793 SNORA2A 0.004141989 2.47 2.89 1.33 BrAr:LOC619569_at LOC619569 SNORA41 0.005258597 4.34 5.33 1.98 BrAr:LOC112574_at LOC112574 SNX18 0.005169055 4.89 5.34 1.37 BrAr:LOC124460_at LOC124460 SNX20 3.26962E−06 2.68 3.02 1.26 BrAr:LOC55553_at LOC55553 SOX6 0.006451258 4.9 3.77 0.46 BrAr:LOC6662_at LOC6662 SOX9 0.009655204 6.9 5.72 0.44 BrAr:LOC6672_at LOC6672 SP100 0.001727009 6.96 7.45 1.4 BrAr:LOC6688_at LOC6688 SPI1 0.008822213 4.24 4.76 1.43 BrAr:LOC6708_at LOC6708 SPTA1 1.16906E−06 2.38 3.23 1.81 BrAr:LOC6711_at LOC6711 SPTBN1 0.008787825 7.9 7.37 0.69 BrAr:LOC55133_at LOC55133 SRBD1 7.08163E−05 5.76 6.1 1.27 BrAr:LOC57522_at LOC57522 SRGAP1 0.003087427 5.55 5.17 0.77 BrAr:LOC5552_at LOC5552 SRGN 0.00272892 8.12 9.19 2.1 BrAr:LOC6728_at LOC6728 SRP19 0.003493429 7.37 7.85 1.39 BrAr:LOC54434_at LOC54434 SSH1 0.005981539 4.52 4.85 1.26 BrAr:LOC6775_at LOC6775 STAT4 0.005220669 4.41 5.34 1.9 BrAr:LOC6793_at LOC6793 STK10 0.009263738 4.53 5.12 1.51 BrAr:LOC6789_at LOC6789 STK4 0.00450869 7.93 8.48 1.47 BrAr:LOC8676_at LOC8676 STX11 0.00051139 3.55 4.29 1.68 BrAr:LOC252983_at LOC252983 STXBP4 0.001970755 5.31 4.7 0.65 BrAr:LOC84144_at LOC84144 SYDE2 0.003504369 4.13 3.2 0.52 BrAr:LOC6856_at LOC6856 SYPL1 0.001398608 9.2 8.65 0.68 BrAr:LOC23118_at LOC23118 TAB2 0.008891674 7.08 7.48 1.33 BrAr:LOC10579_at LOC10579 TACC2 0.004608709 4.74 3.94 0.57 BrAr:LOC117289_at LOC117289 TAGAP 0.000123163 4.2 5.36 2.24 BrAr:LOC51347_at LOC51347 TAOK3 0.007575933 6.88 7.21 1.26 BrAr:LOC374403_at LOC374403 TBC1D10C 3.27706E−06 3.27 4.3 2.05 BrAr:LOC55357_at LOC55357 TBC1D2 0.003377907 4.63 5.44 1.75 BrAr:LOC29110_at LOC29110 TBK1 0.004923083 6.36 6.71 1.27 BrAr:LOC79718_at LOC79718 TBL1XR1 0.000559181 8.66 8.14 0.7 BrAr:LOC57057_at LOC57057 TBX20 7.90703E−05 3.2 3.93 1.66 BrAr:LOC30009_at LOC30009 TBX21 0.007593459 3.96 4.8 1.79 BrAr:LOC7003_at LOC7003 TEAD1 1.21964E−05 7.54 6.73 0.57 BrAr:LOC9840_at LOC9840 TESPA1 0.001195878 3.32 4.15 1.79 BrAr:LOC29844_at LOC29844 TFPT 0.000897111 8.52 8.96 1.35 BrAr:LOC80764_at LOC80764 THAP7 0.005395763 2.81 3.13 1.25 BrAr:LOC387357_at LOC387357 THEMIS 0.001717237 4.43 5.77 2.52 BrAr:LOC9473_at LOC9473 THEMIS2 0.002444402 4.13 4.95 1.76 BrAr:LOC79896_at LOC79896 THNSL1 0.005476544 3.76 3.29 0.72 BrAr:LOC7072_at LOC7072 TIA1 0.00561477 5.85 6.3 1.36 BrAr:LOC201633_at LOC201633 TIGIT 0.001834122 3.26 4.23 1.95 BrAr:LOC9414_at LOC9414 TJP2 0.007201227 6.02 5.42 0.66 BrAr:LOC140711_at LOC140711 TLDC2 0.008125954 3.2 3.53 1.26 BrAr:LOC7099_at LOC7099 TLR4 0.006243027 6.74 7.4 1.58 BrAr:LOC10333_at LOC10333 TLR6 0.006729152 3.05 3.52 1.39 BrAr:LOC54106_at LOC54106 TLR9 0.004792073 2.51 2.83 1.25 BrAr:LOC53346_at LOC53346 TM6SF1 0.001782749 4.48 5.11 1.56 BrAr:LOC147138_at LOC147138 TMC8 0.001322432 3.09 3.58 1.41 BrAr:LOC201799_at LOC201799 TMEM154 0.006931541 3.57 4.69 2.17 BrAr:LOC132332_at LOC132332 TMEM155 0.002173193 2.02 2.96 1.91 BrAr:LOC80008_at LOC80008 TMEM156 0.003752351 2.89 3.68 1.73 BrAr:LOC23731_at LOC23731 TMEM245 0.004802032 6.91 6.32 0.66 BrAr:LOC84302_at LOC84302 TMEM246 0.004460952 5.12 4.03 0.47 BrAr:LOC144110_at LOC144110 TMEM86A 0.000526517 4.01 4.51 1.41 BrAr:LOC252839_at LOC252839 TMEM9 0.006039341 6.71 6.2 0.7 BrAr:LOC7126_at LOC7126 TNFAIP1 0.003724845 6.07 5.59 0.72 BrAr:LOC7127_at LOC7127 TNFAIP2 0.007086897 3.8 4.2 1.33 BrAr:LOC79626_at LOC79626 TNFAIP8L2 0.005171815 5.38 6.27 1.86 BrAr:LOC8764_at LOC8764 TNFRSF14 0.000685645 4.93 5.3 1.29 BrAr:LOC10673_at LOC10673 TNFSF13B 0.000330647 7.04 8.27 2.33 BrAr:LOC944_at LOC944 TNFSF8 0.000583173 3.78 4.65 1.82 BrAr:LOC10040_at LOC10040 TOM1L1 0.006200634 7.15 6.13 0.49 BrAr:LOC9804_at LOC9804 TOMM20 0.003122245 8.31 7.83 0.72 BrAr:LOC163590_at LOC163590 TORlAIP2 0.005250439 5.01 4.46 0.68 BrAr:LOC9760_at LOC9760 TOX 0.009969532 2.93 3.71 1.72 BrAr:LOC58476_at LOC58476 TP53INP2 0.002403891 6.48 5.84 0.64 BrAr:LOC28755_at LOC28755 TRAC 0.003798506 6.57 8.11 2.9 BrAr:LOC7185_at LOC7185 TRAF1 0.002177656 3.39 4 1.53 BrAr:LOC80342_at LOC80342 TRAF3IP3 0.000221585 4.47 5.34 1.83 BrAr:LOC28737_at LOC28737 TRAJ18 0.000140457 2.62 3.48 1.82 BrAr:LOC9881_at LOC9881 TRANK1 0.000942584 4.84 5.54 1.63 BrAr:LOC10131_at LOC10131 TRAP1 0.009156509 7.5 6.81 0.62 BrAr:LOC50852_at LOC50852 TRAT1 0.003755808 4.24 5.69 2.73 BrAr:LOC28688_at LOC28688 TRAYS 2.09643E−06 2.61 3.4 1.73 BrAr:LOC28638_at LOC28638 TRBC2 0.006293187 8.36 9.86 2.83 BrAr:LOC23321_at LOC23321 TRIM2 0.000863602 6.54 5.4 0.46 BrAr:LOC6737_at LOC6737 TRIM21 0.003545744 6.49 7.02 1.45 BrAr:LOC10346_at LOC10346 TRIM22 0.000567832 7.55 8.35 1.74 BrAr:LOC140691_at LOC140691 TRIM69 0.008249984 2.96 3.37 1.33 BrAr:LOC83707_at LOC83707 TRPT1 0.002909746 5.65 6.16 1.42 BrAr:LOC51393_at LOC51393 TRPV2 0.002776554 4.44 4.97 1.45 BrAr:LOC23554_at LOC23554 TSPAN12 0.008216589 8.56 7.09 0.36 BrAr:LOC164118_at LOC164118 TTC24 0.000150934 2.42 2.89 1.38 BrAr:LOC23331_at LOC23331 TTC28 0.00335618 5.76 5 0.59 BrAr:LOC7286_at LOC7286 TUFT1 0.005760063 3.8 3.26 0.69 BrAr:LOC7289_at LOC7289 TULP3 0.007323623 6.12 5.62 0.71 BrAr:LOC11344_at LOC11344 TWF2 0.001857556 5.47 6.02 1.47 BrAr:LOC7305_at LOC7305 TYROBP 0.002745226 9.37 10.17 1.75 BrAr:LOC199746_at LOC199746 U2AF1L4 0.003606119 4.42 5 1.5 BrAr:LOC283991_at LOC283991 UBALD2 0.005670187 4.96 5.5 1.45 BrAr:LOC53347_at LOC53347 UBASH3A 2.71583E−05 2.78 3.2 1.34 BrAr:LOC56061_at LOC56061 UBFD1 0.001588397 7.25 6.62 0.65 BrAr:LOC7372_at LOC7372 UMPS 0.007796438 6.4 5.96 0.74 BrAr:LOC7391_at LOC7391 USF1 0.001182734 3.98 4.43 1.36 BrAr:LOC9958_at LOC9958 USP15 0.000863058 6.45 7 1.46 BrAr:LOC158880_at LOC158880 USP51 0.002422567 3.63 3.3 0.79 BrAr:LOC6843_at LOC6843 VAMP1 0.000736222 2.86 3.27 1.32 BrAr:LOC9217_at LOC9217 VAPB 8.55226E−05 6.91 6.38 0.69 BrAr:LOC7409_at LOC7409 VAV1 0.000186062 4.59 5.72 2.19 BrAr:LOC7716_at LOC7716 VEZF1 0.001044986 6.93 6.53 0.76 BrAr:LOC7443_at LOC7443 VRK1 0.002220519 6.75 7.33 1.5 BrAr:LOC284415_at LOC284415 VSTM1 6.7987E−05 2.86 3.67 1.76 BrAr:LOC7454_at LOC7454 WAS 0.000745019 4.52 5.31 1.73 BrAr:LOC8976_at LOC8976 WASL 6.45542E−05 5.9 5.26 0.64 BrAr:LOC7456_at LOC7456 WIPF1 0.0016442 7.26 8.05 1.72 BrAr:LOC26118_at LOC26118 WSB1 0.004722578 8.36 9 1.56 BrAr:LOC23286_at LOC23286 WWC1 9.72052E−05 7.29 5.56 0.3 BrAr:LOC25937_at LOC25937 WWTR1 0.000418593 8.84 8.39 0.73 BrAr:LOC63929_at LOC63929 XPNPEP3 0.00882263 5.45 5 0.73 BrAr:LOC9942_at LOC9942 XYLB 0.000620581 5.24 4.4 0.56 BrAr:LOC10413_at LOC10413 YAP1 0.000471948 6.52 5.7 0.57 BrAr:LOC7535_at LOC7535 ZAP70 2.17013E−05 3.26 3.87 1.53 BrAr:LOC79413_at LOC79413 ZBED2 0.002690869 3.04 4.13 2.13 BrAr:LOC81030_at LOC81030 ZBP1 0.001365506 3.1 3.63 1.44 BrAr:LOC65986_at LOC65986 ZBTB10 6.24155E−05 6.03 5.22 0.57 BrAr:LOC29068_at LOC29068 ZBTB44 0.006051218 8.48 7.94 0.69 BrAr:LOC340152_at LOC340152 ZC3H12D 0.002391622 2.94 3.29 1.28 BrAr:LOC92092_at LOC92092 ZC3HAV1L 0.002285154 7 6.14 0.55 BrAr:LOC79670_at LOC79670 ZCCHC6 0.00012791 6.4 7.13 1.67 BrAr:LOC84243_at LOC84243 ZDHHC18 0.009930106 4.15 4.66 1.42 BrAr:LOC7538_at LOC7538 ZFP36 0.002038195 5.92 6.66 1.67 BrAr:LOC346171_at LOC346171 ZFP57 0.006254335 2.86 3.22 1.28 BrAr:LOC9372_at LOC9372 ZFYVE9 0.00211562 5.54 5.01 0.69 BrAr:LOC84619_at LOC84619 ZGPAT 0.004266495 4.55 4.92 1.29 BrAr:LOC22882_at LOC22882 ZHX2 0.001424801 9.54 8.88 0.63 BrAr:LOC7586_at LOC7586 ZKSCAN1 0.003281465 5.98 5.51 0.72 BrAr:LOC84225_at LOC84225 ZMYND15 0.000116904 2.69 3.14 1.36 BrAr:LOC94039_at LOC94039 ZNF101 0.000182538 4.92 5.85 1.9 BrAr:LOC7566_at LOC7566 ZNF18 0.001440453 3.13 3.54 1.33 BrAr:LOC286101_at LOC286101 ZNF252P 0.000891302 5.82 5.18 0.64 BrAr:LOC10308_at LOC10308 ZNF267 0.009630783 6.54 7.13 1.5 BrAr:LOC92822_at LOC92822 ZNF276 0.001512078 3.48 3.87 1.32 BrAr:LOC63925_at LOC63925 ZNF335 0.000953752 2.98 3.42 1.36 BrAr:LOC84124_at LOC84124 ZNF394 0.000427762 5.04 5.4 1.29 BrAr:LOC58499_at LOC58499 ZNF462 6.00777E−05 6.84 5.92 0.53 BrAr:LOC144348_at LOC144348 ZNF664 0.001903398 7.66 7.2 0.73 BrAr:LOC79970_at LOC79970 ZNF767 0.000764983 3.37 3.97 1.52 BrAr:LOC128611_at LOC128611 ZNF831 2.84292E−05 2.91 3.3 1.31 BrAr:LOC84937_at LOC84937 ZNRF1 0.005882736 4.42 4.79 1.29 BrAr:LOC84133_at LOC84133 ZNRF3 0.00270792 3.31 2.57 0.6 BrAr:LOC79699_at LOC79699 ZYG11B 0.009608898 5.57 5.13 0.74

TABLE 7B Normalization of select genes presented in Table 7A relative to the mean of all values measured at baseline. Categorization of response NKG7 PVRIG SPI1 CLEC2B TNFSF13B CTLA4 TIGIT NKTR CD244 PDCD1LG2 TNFRSF14 TNFSF8 ≥20% decrease 8.63 8.43 4.87 9.19 8.96 4.88 4.48 6.93 4.19 5.73 6.06 5.48 ≥20% decrease 8.60 7.98 5.44 8.56 8.62 5.51 4.79 5.74 4.59 4.63 5.24 4.40 ≥20% decrease 7.91 8.28 5.88 8.64 8.35 3.55 4.17 6.21 4.93 6.42 5.44 5.55 ≥20% decrease 7.39 7.38 4.49 8.69 7.80 3.61 3.58 5.78 3.38 4.57 4.75 3.59 ≥20% decrease 7.50 7.69 4.80 8.18 9.29 4.69 4.60 5.75 4.00 6.58 5.60 5.43 ≥20% decrease 9.71 10.07 5.69 8.30 8.97 5.50 6.50 6.28 5.38 6.77 6.18 5.95 ≥20% decrease 9.23 10.06 4.63 8.99 8.25 5.20 5.17 6.09 4.68 5.51 5.08 5.69 RMA intensity value at C2D8 ≥20% decrease 7.72 7.14 3.82 6.65 6.67 3.27 3.06 5.38 3.52 4.08 5.20 3.21 ≥20% decrease 8.19 7.94 4.96 7.62 8.50 4.51 4.67 5.38 3.92 6.36 5.19 4.90 ≥20% decrease 8.02 7.16 4.67 8.58 8.61 4.86 4.39 5.99 4.39 5.88 5.58 4.60 ≥20% decrease 6.79 7.88 4.10 8.86 8.42 4.89 2.97 5.20 3.28 4.89 5.04 3.85 <20% decrease 6.79 6.49 4.06 8.25 7.14 3.34 2.93 5.62 3.10 3.68 5.14 3.36 <20% decrease 4.68 5.55 4.30 6.34 6.77 2.92 2.36 5.10 3.44 3.64 5.16 4.01 <20% decrease 6.28 5.96 3.74 7.83 6.95 3.83 3.47 6.92 3.09 4.85 5.49 4.03 <20% decrease 5.39 6.65 4.91 7.34 7.29 3.05 2.68 6.39 3.29 4.16 5.03 3.75 <20% decrease 6.34 6.64 3.96 6.80 7.32 3.53 3.45 5.69 2.90 3.98 4.78 3.23 <20% decrease 6.54 7.37 4.07 6.44 6.70 3.36 3.39 4.42 3.38 3.46 5.12 3.43 <20% decrease 6.89 7.46 4.44 8.00 8.80 3.31 3.17 5.00 3.46 5.20 4.92 4.46 <20% decrease 6.37 6.54 4.23 6.27 5.66 2.89 2.83 5.10 3.18 3.25 5.16 3.64 <20% decrease 5.27 5.15 4.10 7.67 6.47 3.62 3.07 5.40 2.77 4.14 5.37 3.48 <20% decrease 4.59 5.94 3.99 6.75 5.30 2.83 2.60 5.80 3.05 2.70 4.16 3.12 <20% decrease 7.67 6.63 4.83 8.36 8.46 3.83 3.74 5.16 4.12 5.33 4.81 4.47 <20% decrease 8.24 7.99 4.63 7.68 8.21 5.43 4.86 6.03 4.02 6.50 5.10 4.62 <20% decrease 7.00 8.06 5.09 7.52 8.55 3.60 3.90 5.48 3.66 5.90 4.69 4.52 <20% decrease 5.76 6.93 4.07 7.11 7.76 3.19 3.19 5.83 3.41 4.34 4.46 3.67 <20% decrease 7.54 7.58 5.25 7.91 9.05 5.87 4.07 5.60 4.49 7.66 5.03 4.88 <20% decrease 8.99 8.04 4.06 8.20 8.32 4.15 4.71 4.56 4.77 5.42 5.69 5.20 <20% decrease 5.02 5.87 4.19 8.98 6.97 3.26 2.83 4.69 2.98 3.35 5.32 3.10 <20% decrease 5.90 5.52 3.64 6.50 5.98 2.93 2.71 6.18 2.97 3.37 4.72 3.80 <20% decrease 8.00 7.89 4.93 7.82 7.21 3.97 4.73 5.95 6.14 6.66 5.29 4.98 <20% decrease 9.31 8.89 5.11 8.16 8.88 6.05 5.40 4.94 5.01 6.70 5.26 4.42 <20% decrease 8.61 8.77 5.65 8.67 9.15 6.36 5.51 5.86 4.80 6.46 5.45 5.71 <20% decrease 5.63 6.19 4.13 6.83 5.67 2.97 2.67 4.97 3.38 3.86 4.98 3.34 <20% decrease 5.76 5.83 4.19 8.96 7.22 3.51 3.04 5.47 3.36 4.04 4.51 3.83 <20% decrease 5.81 5.99 3.99 6.82 6.10 3.09 2.97 5.08 3.06 3.44 4.91 3.64 <20% decrease 7.69 7.78 5.09 8.05 9.12 5.70 5.12 5.77 3.70 7.03 5.21 5.14 <20% decrease 5.58 6.08 4.50 6.54 6.28 3.36 3.17 4.64 3.06 3.20 4.08 3.38 <20% decrease 5.37 5.70 4.48 6.98 6.55 2.95 2.71 5.69 3.26 3.44 4.71 3.75 <20% decrease 8.28 7.38 4.28 8.21 8.34 5.34 4.73 5.88 3.56 6.34 5.06 4.72 <20% decrease 5.95 6.50 4.12 7.18 6.79 3.14 2.61 4.73 2.94 3.95 4.53 3.64 <20% decrease 6.11 6.16 4.55 8.67 7.66 2.94 2.63 5.19 2.96 3.63 4.96 3.74 <20% decrease 6.57 5.80 4.19 6.50 6.54 2.79 3.19 5.56 3.72 4.76 4.99 4.55 <20% decrease 5.76 5.62 4.13 7.45 6.58 3.97 2.97 5.45 3.06 4.65 4.82 3.74 <20% decrease 5.37 6.19 4.40 6.48 5.81 3.08 2.86 5.21 3.31 3.70 4.84 2.91 <20% decrease 6.87 8.10 4.95 7.71 8.74 4.59 5.23 5.09 3.58 5.40 5.47 4.40 <20% decrease 7.36 6.77 4.50 7.77 6.96 3.29 3.68 6.04 3.67 3.70 5.09 4.05 <20% decrease 5.45 5.48 4.01 7.17 7.00 2.85 2.44 4.80 3.24 3.58 4.86 3.18 <20% decrease 6.85 5.88 4.65 7.76 7.91 3.90 3.62 5.84 3.63 4.66 4.56 4.10 <20% decrease 6.35 6.35 3.80 6.14 7.44 3.26 2.96 5.00 3.25 4.70 4.95 3.51 <20% decrease 7.97 7.90 4.69 8.11 7.63 3.94 3.80 4.47 3.68 5.68 4.70 4.33 <20% decrease 6.52 6.41 3.77 7.13 6.56 3.68 3.89 6.20 3.27 3.90 5.33 3.76 <20% decrease 7.86 7.34 4.62 8.57 8.59 4.67 4.54 5.30 4.59 5.88 5.03 4.09 <20% decrease 6.32 6.35 5.10 8.83 6.72 3.23 2.92 5.22 3.01 4.58 4.90 3.71 <20% decrease 5.54 6.21 3.67 6.42 6.37 3.34 2.87 6.31 2.98 3.92 4.49 3.37 <20% decrease 7.12 5.46 3.42 6.46 5.73 2.74 2.69 4.42 3.52 3.85 5.66 3.10 Mean RMA, 6.89 6.97 4.47 7.66 7.48 3.89 3.66 5.50 3.67 4.80 5.06 4.12 all Patients Mean RMA, 8.15 8.18 4.85 8.39 8.40 4.59 4.40 5.88 4.21 5.58 5.40 4.79 Responders Fold-difference 2.40 2.31 1.30 1.65 1.89 1.62 1.67 1.30 1.45 1.72 1.26 1.59 in Mean values Expression relative to Mean of all values at C2D8 <20% decrease 3.35 2.74 1.32 2.87 2.78 1.99 1.76 2.69 1.43 1.90 2.01 2.56 <20% decrease 3.27 2.01 1.96 1.86 2.19 3.06 2.19 1.18 1.89 0.89 1.13 1.21 <20% decrease 2.03 2.47 2.66 1.96 1.82 0.79 1.43 1.63 2.39 3.07 1.30 2.69 <20% decrease 1.42 1.33 1.02 2.04 1.24 0.82 0.95 1.21 0.82 0.85 0.81 0.70 <20% decrease 1.52 1.64 1.26 1.43 3.49 1.74 1.92 1.18 1.25 3.43 1.45 2.48 <20% decrease 7.08 8.60 2.33 1.55 2.80 3.04 7.15 1.71 3.27 3.92 2.17 3.57 >20% decrease 5.06 8.49 1.12 2.51 1.70 2.48 2.84 1.50 2.00 1.63 1.02 2.97 >20% decrease 1.78 1.12 0.64 0.49 0.57 0.65 0.66 0.92 0.90 0.61 1.11 0.53 >20% decrease 2.46 1.96 1.40 0.97 2.02 1.53 2.02 0.92 1.18 2.94 1.10 1.72 >20% decrease 2.20 1.14 1.15 1.89 2.18 1.96 1.66 1.40 1.65 2.11 1.43 1.39 >20% decrease 0.93 1.88 0.77 2.29 1.92 1.99 0.62 0.81 0.76 1.07 0.99 0.83 <20% decrease 0.94 0.72 0.75 1.50 0.79 0.68 0.60 1.09 0.67 0.46 1.06 0.59 <20% decrease 0.22 0.37 0.89 0.40 0.61 0.51 0.41 0.76 0.85 0.45 1.08 0.93 <20% decrease 0.65 0.50 0.60 1.12 0.69 0.96 0.88 2.66 0.67 1.04 1.35 0.94 <20% decrease 0.35 0.80 1.36 0.80 0.88 0.56 0.51 1.84 0.76 0.64 0.98 0.77 <20% decrease 0.68 0.79 0.70 0.55 0.89 0.78 0.87 1.13 0.59 0.57 0.82 0.54 <20% decrease 0.78 1.32 0.76 0.43 0.58 0.69 0.83 0.47 0.82 0.40 1.04 0.62 <20% decrease 1.00 1.41 0.98 1.26 2.49 0.67 0.71 0.71 0.86 1.32 0.91 1.27 <20% decrease 0.70 0.74 0.85 0.38 0.28 0.50 0.56 0.75 0.71 0.34 1.08 0.72 <20% decrease 0.32 0.28 0.77 1.00 0.50 0.83 0.66 0.93 0.53 0.63 1.24 0.64 <20% decrease 0.20 0.49 0.72 0.53 0.22 0.48 0.48 1.23 0.65 0.23 0.54 0.50 <20% decrease 1.71 0.79 1.28 1.62 1.97 0.96 1.05 0.79 1.36 1.45 0.84 1.28 <20% decrease 2.56 2.03 1.12 1.01 1.65 2.90 2.29 1.44 1.27 3.26 1.03 1.42 <20% decrease 1.08 2.13 1.54 0.90 2.10 0.82 1.18 0.98 0.99 2.15 0.78 1.32 <20% decrease 0.46 0.97 0.76 0.68 1.21 0.62 0.72 1.25 0.83 0.73 0.66 0.74 <20% decrease 1.57 1.52 1.72 1.19 2.95 3.94 1.33 1.07 1.76 7.26 0.98 1.70 <20% decrease 4.29 2.10 0.75 1.45 1.78 1.20 2.07 0.52 2.13 1.54 1.55 2.11 <20% decrease 0.27 0.47 0.82 2.49 0.70 0.64 0.56 0.57 0.62 0.37 1.20 0.49 <20% decrease 0.50 0.37 0.56 0.45 0.35 0.51 0.52 1.60 0.61 0.37 0.79 0.80 <20% decrease 2.15 1.89 1.37 1.11 0.83 1.05 2.10 1.36 5.53 3.64 1.18 1.81 <20% decrease 5.36 3.77 1.55 1.40 2.63 4.45 3.33 0.68 2.52 3.72 1.15 1.23 <20% decrease 3.30 3.47 2.27 2.00 3.18 5.54 3.62 1.28 2.19 3.16 1.31 3.01 <20% decrease 0.42 0.58 0.79 0.56 0.28 0.53 0.50 0.69 0.81 0.52 0.94 0.58 <20% decrease 0.46 0.45 0.82 2.45 0.83 0.77 0.65 0.97 0.81 0.59 0.69 0.82 <20% decrease 0.47 0.51 0.72 0.56 0.38 0.57 0.62 0.74 0.65 0.39 0.90 0.72 <20% decrease 1.74 1.76 1.54 1.31 3.11 3.49 2.75 1.20 1.02 4.69 1.11 2.03 <20% decrease 0.40 0.54 1.02 0.46 0.43 0.69 0.71 0.55 0.65 0.33 0.51 0.60 <20% decrease 0.35 0.41 1.01 0.62 0.52 0.52 0.52 1.14 0.75 0.39 0.78 0.77 <20% decrease 2.61 1.33 0.88 1.46 1.81 2.73 2.10 1.29 0.93 2.91 1.00 1.52 <20% decrease 0.52 0.72 0.78 0.72 0.62 0.59 0.48 0.58 0.60 0.55 0.69 0.72 <20% decrease 0.58 0.57 1.06 2.01 1.13 0.52 0.49 0.80 0.61 0.44 0.94 0.77 <20% decrease 0.80 0.44 0.83 0.45 0.52 0.46 0.72 1.04 1.04 0.97 0.96 1.35 <20% decrease 0.46 0.39 0.79 0.86 0.54 1.05 0.62 0.96 0.65 0.90 0.85 0.77 <20% decrease 0.35 0.58 0.95 0.44 0.31 0.57 0.58 0.82 0.78 0.46 0.86 0.43 <20% decrease 0.98 2.19 1.40 1.03 2.39 1.63 2.96 0.75 0.94 1.51 1.33 1.21 <20% decrease 1.38 0.87 1.02 1.07 0.69 0.66 1.01 1.45 0.99 0.47 1.03 0.96 <20% decrease 0.37 0.36 0.73 0.71 0.71 0.48 0.43 0.61 0.74 0.43 0.87 0.52 <20% decrease 0.98 0.47 1.13 1.07 1.34 1.00 0.97 1.26 0.97 0.91 0.71 0.99 <20% decrease 0.69 0.65 0.63 0.35 0.97 0.64 0.62 0.70 0.74 0.93 0.92 0.66 <20% decrease 2.12 1.90 1.16 1.36 1.10 1.03 1.10 0.49 1.00 1.83 0.78 1.16 <20% decrease 0.78 0.68 0.62 0.69 0.53 0.86 1.17 1.62 0.76 0.54 1.21 0.78 <20% decrease 1.95 1.30 1.11 1.87 2.16 1.71 1.84 0.87 1.88 2.11 0.98 0.98 <20% decrease 0.67 0.65 1.55 2.24 0.59 0.63 0.60 0.82 0.63 0.86 0.90 0.75 <20% decrease 0.39 0.59 0.58 0.42 0.46 0.68 0.58 1.75 0.62 0.54 0.67 0.59 <20% decrease 1.17 0.35 0.48 0.43 0.30 0.45 0.51 0.47 0.90 0.52 1.51 0.50

TABLE 8A Genes From an Analysis of Tumor Biopsies With >1.2-fold or <0.8-fold Differences Between Treatment Groups Before and After Treatment Comparing the Fold Change in Responsive and Non-Responsive Subjects. P value for change upon No No treatment Response: Response: Response: Response: No differing Mean Mean Mean Mean Response: Response: HUGO between RMA RMA RMA RMA Change Change Probeset ENTREZ Gene response value at value at value at value at upon upon (BrainArray v.10) Gene ID Symbol groups baseline baseline C2D8 C2D8 treatment treatment BrAr:LOC140_at LOC140 ADORA3 0.003217778 5.64 5.85 5.65 6.72 1 1.83 BrAr:LOC1645_at LOC1645 AKR1C1 0.001911057 7.79 7.23 7.78 5.96 0.99 0.41 BrAr:LOC1646_at LOC1646 AKR1C2 0.000754158 6.14 5.69 6.33 4.63 1.14 0.48 BrAr:LOC57101_at LOC57101 ANO2 0.000361197 2.77 2.58 2.61 3.32 0.9 1.67 BrAr:LOC7984_at LOC7984 ARHGEF5 0.00010372 7.21 6.99 7.18 5.88 0.98 0.46 BrAr:LOC115761_at LOC115761 ARL11 0.003149723 2.94 3.13 2.99 3.59 1.04 1.38 BrAr:LOC445_at LOC445 ASS1 0.000728649 6.91 6.42 6.87 5.75 0.97 0.63 BrAr:LOC23743_at LOC23743 BHMT2 0.00056076 7.41 7.11 7.44 5.77 1.02 0.39 BrAr:LOC80114_at LOC80114 BICC1 0.003236408 6.65 6.16 6.48 5.37 0.89 0.58 BrAr:LOC55337_at LOC55337 C19ORF66 0.001415972 5.39 5.32 5.39 5.83 1 1.42 BrAr:LOC26005_at LOC26005 C2CD3 0.003271581 3.3 3.36 3.24 3.74 0.96 1.3 BrAr:LOC718_at LOC718 C3 0.000510688 10.78 10.93 10.95 10.04 1.12 0.54 BrAr:LOC64170_at LOC64170 CARD9 0.001441216 4.24 4.46 4.38 5.22 1.1 1.69 BrAr:LOC50937_at LOC50937 CDON 0.005728583 4.65 4.23 4.45 3.52 0.87 0.61 BrAr:LOC55501_at LOC55501 CHST12 0.000722334 3.51 3.58 3.47 4.04 0.97 1.38 BrAr:LOC146223_at LOC146223 CMTM4 0.000872911 5.68 5.63 5.54 4.84 0.91 0.58 BrAr:LOC1759_at LOC1759 DNM1 0.000278896 4.86 5.14 4.7 3.89 0.9 0.42 BrAr:LOC1956_at LOC1956 EGFR 0.007012678 7.36 6.8 7.23 5.74 0.92 0.48 BrAr:LOC100131897_at LOC100131897 FAM196B 0.002546233 3.74 3.93 3.72 4.27 0.99 1.27 BrAr:LOC2195_at LOC2195 FAT1 0.009212583 9.67 9.47 9.47 8.45 0.87 0.49 BrAr:LOC115290_at LOC115290 FBXO17 0.001904392 6 5.74 5.9 5 0.93 0.6 BrAr:LOC11328_at LOC11328 FKBP9 0.008901288 6.75 6.49 6.64 6.04 0.93 0.73 BrAr:LOC8321_at LOC8321 FZD1 0.001761088 7.19 6.83 7.17 6.39 0.99 0.73 BrAr:LOC2581_at LOC2581 GALC 6.17362E−05 5.63 5.6 5.7 6.18 1.05 1.5 BrAr:LOC57678_at LOC57678 GPAM 0.001774483 4.9 4.95 5.21 4.31 1.24 0.64 BrAr:LOC3226_at LOC3226 HOXC10 0.003809884 6.97 6.76 6.98 5.74 1.01 0.49 BrAr:LOC9956_at LOC9956 HS3ST2 0.003715771 3.53 3.7 3.39 4.27 0.9 1.49 BrAr:LOC79190_at LOC79190 IRX6 0.000738422 3.31 3.07 3.47 2.69 1.12 0.77 BrAr:LOC3766_at LOC3766 KCNJ10 0.007473696 2.48 2.67 2.8 3.99 1.24 2.49 BrAr:LOC100289455_at LOC100289455 LOC100289455 0.001954644 3.27 3.13 3.29 3.65 1.01 1.44 BrAr:LOC4125_at LOC4125 MAN2B1 0.007502126 6.22 6.64 6.33 7.04 1.08 1.32 BrAr:LOC22823_at LOC22823 MTF2 0.00018303 5.73 5.74 5.75 6.13 1.02 1.31 BrAr:LOC51172_at LOC51172 NAGPA 0.001020819 4.18 4.04 4.11 4.45 0.96 1.33 BrAr:LOC10787_at LOC10787 NCKAP1 0.009526855 8.51 8.26 8.41 7.77 0.93 0.71 BrAr:LOC23413_at LOC23413 NCS1 0.00077159 5.16 5.07 5.17 4.65 1.01 0.75 BrAr:LOC4820_at LOC4820 NKTR 0.005837122 5.46 5.54 5.41 6.03 0.97 1.41 BrAr:LOC80896_at LOC80896 NPL 0.003423516 5.66 6.09 5.67 6.94 1 1.81 BrAr:LOC375387_at LOC375387 NRROS 0.001100607 4.17 4.25 4.04 4.69 0.91 1.36 BrAr:LOC79668_at LOC79668 PARP8 0.001671059 5.48 5.7 5.58 6.21 1.07 1.43 BrAr:LOC197135_at LOC197135 PATL2 6.9616E−05 3.06 2.98 3.01 3.59 0.97 1.53 BrAr:LOC9033_at LOC9033 PKD2L1 0.004494258 3.82 4.2 3.89 4.98 1.05 1.72 BrAr:LOC5729_at LOC5729 PTGDR 0.002150214 2.38 2.33 2.38 2.81 1 1.4 BrAr:LOC10235_at LOC10235 RASGRP2 0.003641911 3.05 3.12 2.92 3.68 0.92 1.48 BrAr:LOC5973_at LOC5973 RENBP 0.009590131 2.31 2.38 2.38 2.75 1.05 1.29 BrAr:LOC55599_at LOC55599 RNPC3 0.003973794 5.09 5.03 5.01 5.72 0.94 1.61 BrAr:LOC57337_at LOC57337 SENP7 0.001110208 4.54 4.43 4.38 4.86 0.9 1.35 BrAr:LOC166929_at LOC166929 SGMS2 0.002683966 5.19 5.12 4.98 4.48 0.87 0.64 BrAr:LOC11309_at LOC11309 SLCO2B1 0.006057789 4.53 4.85 4.67 5.2 1.1 1.28 BrAr:LOC6708_at LOC6708 SPTA1 0.005000147 2.36 2.55 2.38 3.23 1.01 1.6 BrAr:LOC7003_at LOC7003 TEAD1 0.00098282 7.6 7.23 7.54 6.73 0.96 0.71 BrAr:LOC144110_at LOC144110 TMEM86A 0.009256951 3.91 4.12 4.01 4.51 1.07 1.31 BrAr:LOC944_at LOC944 TNFSF8 0.002299197 3.68 4.05 3.78 4.65 1.07 1.51 BrAr:LOC10413_at LOC10413 YAP1 0.005339969 6.55 6.26 6.52 5.7 0.98 0.68 BrAr:LOC65986_at LOC65986 ZBTB10 0.002210855 6.11 5.72 6.03 5.22 0.95 0.71 BrAr:LOC9372_at LOC9372 ZFYVE9 0.005927672 5.63 5.39 5.54 5.01 0.94 0.77 BrAr:LOC79970_at LOC79970 ZNF767 0.004796367 3.5 3.58 3.37 3.97 0.91 1.31

TABLE 8B Normalization of select genes presented in Table 8A relative to the mean of all values measured at baseline. RMA intensity RMA intensity Fold change Categorization value at Baseline value at C2D8 on treatment of response NKTR TNFSF8 NKTR TNFSF8 NKTR TNFSF8 ≥20% decrease 3.96 2.68 5.20 3.85 2.4 2.3 ≥20% decrease 5.18 5.08 5.38 4.90 1.2 0.9 ≥20% decrease 5.71 4.57 5.75 5.43 1.0 1.8 ≥20% decrease 5.17 3.48 5.78 3.59 1.5 1.1 ≥20% decrease 5.44 4.57 5.99 4.60 1.5 1.0 ≥20% decrease 4.57 5.12 6.09 5.69 2.9 1.5 ≥20% decrease 6.38 5.38 6.21 5.55 0.9 1.1 ≥20% decrease 5.61 3.55 6.28 5.95 1.6 5.3 ≥20% decrease 6.70 4.32 6.93 5.48 1.2 2.2 <20% decrease 4.76 3.42 4.42 3.10 0.8 0.8 <20% decrease 4.10 3.38 4.42 3.43 1.3 1.0 <20% decrease 5.16 2.99 4.47 4.33 0.6 2.5 <20% decrease 5.10 5.33 4.56 5.20 0.7 0.9 <20% decrease 5.65 4.10 4.69 3.10 0.5 0.5 <20% decrease 4.57 2.77 4.80 3.18 1.2 1.3 <20% decrease 4.45 3.31 4.94 4.42 1.4 2.2 <20% decrease 5.36 3.56 4.97 3.34 0.8 0.9 <20% decrease 5.14 2.61 5.00 3.51 0.9 1.9 <20% decrease 5.01 4.92 5.00 4.46 1.0 0.7 <20% decrease 5.10 3.23 5.08 3.64 1.0 1.3 <20% decrease 4.85 3.83 5.09 4.40 1.2 1.5 <20% decrease 5.57 3.25 5.10 3.64 0.7 1.3 <20% decrease 5.03 4.56 5.10 4.01 1.0 0.7 <20% decrease 4.81 3.90 5.16 4.47 1.3 1.5 <20% decrease 5.64 4.28 5.19 3.74 0.7 0.7 <20% decrease 3.96 3.36 5.21 2.91 2.4 0.7 <20% decrease 5.01 3.38 5.22 3.71 1.2 1.3 <20% decrease 5.47 3.58 5.30 4.09 0.9 1.4 <20% decrease 4.84 4.15 5.47 3.83 1.5 0.8 <20% decrease 5.69 4.97 5.48 4.52 0.9 0.7 <20% decrease 5.25 4.44 5.56 4.55 1.2 1.1 <20% decrease 6.66 3.94 5.60 4.88 0.5 1.9 <20% decrease 5.57 3.85 5.77 5.14 1.2 2.5 <20% decrease 5.38 3.12 5.80 3.12 1.3 1.0 <20% decrease 5.68 3.51 5.83 3.67 1.1 1.1 <20% decrease 5.68 4.37 5.84 4.10 1.1 0.8 <20% decrease 5.36 4.47 5.86 5.71 1.4 2.4 <20% decrease 5.37 4.25 5.88 4.72 1.4 1.4 <20% decrease 6.00 5.36 6.03 4.62 1.0 0.6 <20% decrease 6.33 4.30 6.18 3.80 0.9 0.7 <20% decrease 6.82 3.42 6.31 3.37 0.7 1.0 <20% decrease 5.85 3.60 6.39 3.75 1.4 1.1

D. Safety Analysis

All recorded AEs were listed and tabulated by system organ class, preferred term, treatment group, and dose, and coded according to the most current version of the Medical Dictionary for Regulatory Activities (MedDRA; version 17.1 at database lock). The incidence of AEs was tabulated and reviewed for significance and clinical importance. Summaries of select AEs regardless of causality were created and frequency distributions were tabulated by dose.

III. Results A. Patient Population

Patients were enrolled from September 2011 to September 2012 at 14 participating US and non-US centers. In total, 92 patients were assigned to study treatment, 91 of whom were treated (FIG. 2). The median age of patients was 61 years, 67% were male, and 96% had undergone previous surgery on the primary tumor (Table 9). Baseline characteristics were similar between previously treated patients (n=67), who were assigned to nivolumab 0.3, 2.0, or 10 mg/kg, and treatment-naïve (n=24) patients, who were assigned to nivolumab 10 mg/kg every 3 weeks (Table 9).

TABLE 9 Baseline Patient Characteristics and Demographics. Treatment- Previously Treated, naïve, Nivolumab 0.3, 2, Nivolumab and 10 mg/kg 10 mg/kg Total (n = 67) (n = 24) (n = 91) Median age, years 61.0 63.5 61.0 Sex, n (%) Male 46 (69) 15 (63) 61 (67) Female 21 (31)  9 (38) 30 (33) Previous therapy, n (%) Surgery 64 (96) 23 (96) 87 (96) Radiotherapy 25 (37)  5 (21) 30 (33) Previous systemic therapy  67 (100) 0 67 (74) Therapy for metastatic 60 (90) 0 60 (66) disease Adjuvant therapy 5 (7) 0 5 (6) Neoadjuvant therapy 5 (7) 0 5 (6)

B. Clinical Efficacy

Responses were evaluated in 91 patients who received at least one dose of nivolumab. The ORR was 15% (95% confidence interval (CI), 8.7-24.5) overall; ORRs for individual dose groups are shown in Table 10. Stable disease was observed in 46% of patients overall (Table 10). Twenty one patients met the criterion of at least 20% maximal reduction in Tumor Burden sustained for 2 evaluations (used for analysis of the association between Response and gene expression).

TABLE 10 Clinical Efficacy. Treatment- Previously Treated (n = 67) naïve Nivolumab Nivolumab Nivolumab Nivolumab 0.3 mg/kg 2.0 mg/kg 10 mg/kg 10 mg/kg Total (n = 22) (n = 22) (n = 23) (n = 24) (n = 91)^(a) ORR, n (%)^(b) 2 (9)  4 (18)  5 (22)  3 (13) 14 (15) 95% CI 1.1-29.2 5.2-40.3 7.5-43.7 2.7-32.4 8.7-24.5 Best response, n (%) CR 0 0 0 2 (8) 2 (2) PR 2 (9)  4 (18)  5 (22) 1 (4) 12 (13) Stable disease  8 (36) 10 (46) 11 (48) 13 (54) 42 (46) Progressive  9 (41)  5 (23)  6 (26)  7 (29) 27 (30) disease Unable to  3 (14)  3 (14) 1 (4) 1 (4) 8 (9) determine PFS rate, % (95% CI) At 24 weeks NE 44 (23-63) 58 (35-76) 50 (28-68) 43 (32-53) At 48 weeks NE NE 32 (13-52) 39 (18-59) 25 (16-35) OS rate, % (95% CI) At 12 months 71 (47-86) 72 (48-86) 74 (48-88) 81 (57-92) 75 (64-83) At 24 months 44 (22-64) 61 (36-78) 51 (27-71) 76 (51-89) 58 (46-68) Median OS, 16.4 NR 25.2 NR — months (10.1-NR) (12.0-NR) (95% CI) Note ORR, objective response rate; CR, complete response; NE, not evaluated; NR, not reached; PR, partial response; PFS, progression free survival; OS, overall survival. ^(a)All treated patients were evaluated for response. ^(b)Confirmed response only.

Progression-free survival (PFS) rates were 43% (95% CI, 32-53) at 24 weeks and 25% (95% CI, 16-35) at 48 weeks overall; PFS rates for individual dose groups are shown in Table 10.

Overall survival (OS) rates were 75% (95% CI, 64-83) at 12 months and 58% (95% CI, 46-68) at 24 months overall; OS rates for individual dose groups are shown in Table 10 and FIG. 3. Median OS (95% CI) was 16.4 months (95% CI, 10.1—not reached (NR)) for Arm 1 (0.3 mg/kg nivolumab), NR for Arm 2 (2 mg/kg nivolumab), 25.2 months (95% CI, 12.0—NR) for Arm 3 (10 mg/kg nivolumab), and NR for Arm 4 (10 mg/kg nivolumab) patients (Table 10; FIG. 3).

C. Tumor-Associated Lymphocytes

Immunohistochemistry (IHC) of tissue from serial tumor biopsies was performed to evaluate whether frequencies of tumor-associated lymphocytes increased with nivolumab treatment. On-treatment biopsies showed enrichment of CD3+, CD4+, and CD8+ cells from baseline to cycle 2 day 8 (FIG. 4A-FIG. 5G). For all nivolumab-treated patients combined with baseline and cycle 2 day 8 values (N=36), median changes from baseline to cycle 2 day 8 in the proportion of CD3+, CD4+, and CD8+ cells were 9.83%, 0.44%, and 2.64%, respectively, with a majority of patients experiencing increases (FIG. 4E-FIG. 4G). Baseline percentages and increases from baseline were greater for CD3+ and CD8+ than for CD4+ cells. Most patients had very low or undetectable levels of CD4+ at baseline, and only modest changes from baseline. Fourteen patients had both baseline percentages and changes from baseline values <0.45%. Increases were observed across all baseline levels. These results did not appear to vary with nivolumab dose or previous treatment status (data not shown).

Distributions of the proportion of CD3+, CD4+, and CD8+ cells and their relationships to each other are shown in FIG. 5A-FIG. 5F. Changes in the proportion of CD3+ and CD8+ cells were highly associated (FIG. 5B), while changes in the proportion of CD4+ cells did not appear to be associated with changes in CD3+(FIG. 5A) or CD8+(FIG. 5C) cells. Changes in the proportion of CD3+ cells were nearly always greater than changes in the proportion of CD4+(FIG. 5A) or CD8+(FIG. 5B) cells. Expression analysis of RNA from tumor biopsies obtained in parallel showed that CD3 (FIG. 5G) and CD8 (FIG. 5H), but not CD4 (FIG. 5J), transcripts significantly increased post-treatment (1.7-fold for gene CD3D, p=0.006 [FIG. 5G]; 1.7-fold for gene CD8A, p=0.002 [FIG. 5H]; 1.2-fold for gene CD4, p=0.175 [FIG. 5J]). These changes did not appear to depend on nivolumab dose or previous treatment.

D. Receptor Occupancy

Nivolumab occupancy of the PD-1 receptor in peripheral T cells varied negligibly with dose or previous treatment status. Peak median receptor occupancy was 99% (range, 55%-117%) at cycle 1 day 1 at 1 hour after treatment infusion for all patients combined (FIG. 6A-FIG. 6D). Median receptor occupancy at cycle 1 day 1 was 99% for Arm 1 (0.3 mg/kg nivolumab; FIG. 6A), 99% for Arm 2 (2 mg/kg nivolumab; FIG. 6B), and 96% for Arm 3 (10 mg/kg nivolumab; FIG. 6C), and 97% for all previously treated patients combined; and 102% for treatment-naïve patients (Arm 4; 10 mg/kg nivolumab; FIG. 6D). Median PD-1 occupancy was sustained through cycle 8 day 1 for all treatment groups (≥97%) except the 10 mg/kg previously treated group, where a slight decrease in median occupancy to 83% (range, 56%-90%) was observed at cycle 8 day 1 (FIG. 6A-FIG. 6D).

E. PD-L1 Expression and Objective Response

The association between ORR and PD-L1 expression was assessed in fresh biopsies obtained at baseline (Table 11; n=56). The ORR was higher in tumors with ≥5% PD-L1 expression than in tumors with <5% PD-L1 expression ( 4/18 [22%] and 3/38 [8%], respectively). In view of the limited number of patients, the relevance of PD-L1 expression status in RCC tumor cells is to be further investigated.

TABLE 11 Objective Response Rate by PD-L1 Expression. PD-L1 Expression^(a) Fresh tumor samples ≥5% <5% Objective response rate 4/18 (22%) 3/38 (8%) 95% CI 0-60.2% 0-70.8% Note ^(a)Expression is based on tumor membrane staining of tumor biopsies prior to first dose; CI, confidence interval.

F. Gene Expression Profiling

To gain additional insight into the immunological changes in tumors during nivolumab treatment, gene expression profiling was undertaken on baseline and post-treatment tumor biopsies (N=59 at baseline, 55 at cycle 2 day 8, with 42 patients having matched samples). In total, expression of 108 transcripts changed over time based on the significance criteria (>1.3-fold change in mean expression, p<0.01; Table 2, above), including 71 previously associated with immune lineages (Abbas et al. (2005) Genes Immun 6:319-31) (p<0.001), all of which increased at cycle 2 day 8. Of these 71 transcripts, 43 were defined as lymphoid—lineage specific (CD3D, CD3E, CD3G, CD8A, CD8B, CTLA-4, CXCR6, ICOS, TRAT1, ZBED2, CD247, CD69, GZMA, GZMB, GZMH, IFNG, IL2RB, ITK, KLRB1, KLRD1, KLRG1, NKG7, PRF1, STAT4) or myeloid-lineage specific (CASP1, IL1B, CXCL11, IFIH1, UBD, CD274, DAPP1, FGL2, FYB, IDO1, IFIT2, IFITM1, IGSF6, KCNJ2, LILRB1, MREG, P2RY13, TLR8, VNN2) (FIG. 7A). In the lymphoid lineage, an increase was observed for CD8A/B and CD3D/E/G, markers of activated T cells such as CTLA-4 and ICOS, and markers of cytolytic activity such as granzyme A (GZMA) and perforin (PRF1). Transcripts associated with the myeloid lineage include the dendritic cell-associated genes UBD, IFIH1, and CXCL11, the PD-1 ligand PD-L1 (CD274), and the immunomodulatory enzyme IDO1. Sixteen of the 108 transcripts were previously identified as interferon-regulated (Chaussabel et al. (2008) Immunity 29:150-64), including CXCL9 (MIG). Interferon-γ was the only interferon represented in the 108 genes. Pathway analysis of the 108 genes identified significant effects (p<0.001) on interferon signaling, T cell signaling, and major histocompatibility complex class I antigen presentation processes. In particular with reference to major histocompatibility complex class I antigen presentation we observed up-regulation of the immunoproteasome component PSMB9 and the immunopeptide transporter TAP1, and the T cell components VAV1, TRAC, FYB, CD8A, CD8B, CD3G, CD3D, CD3E, CD274 (PDL1) and CD247. The roles of these components are outlined in FIG. 7B.

To evaluate whether similar transcriptional changes were observed in the periphery, microarray analysis was performed on whole blood samples (N=82 at cycle 1 day 1 and N=74 at cycle 1 day 2, with 70 patients having matched samples; N=73 at cycle 2 day 8). Expression of 59 transcripts changed from baseline to cycle 1 day 2 according to the significance criteria (>1.2-fold, p<0.01; Table 3, above), including 30 previously associated with immune lineages (CCR7, CD27, CD3G, IL7R, NFATC3, P2RY8, RORA, TRAC, TRBC2, AIM2, DDX60L, FBXO6, GBP1, GBP5, IFI35, IFI44, IFI6, IFIH1, IFIT1, IFIT2, IFIT3, IRF7, PARP14, PARP9, SAMD9L, SCO2, STAT1, TAP1, TNFAIP6, and TYMP; Abbas et al. (2005) Genes Immun 6:319-31) (p<0.001; FIG. 7C). These included transcripts for T cell receptor α and β subunits and the CD3 γ subunit, which decreased relative to baseline. The 59 transcripts included 29 previously identified as interferon-regulated (Chaussabel et al. (2008) Immunity 29:150-64), all of which increased (indicated by an *; FIG. 7C). No transcripts from interferon genes were regulated or detectable in blood.

With two exceptions, the above transcriptional effects were similar between nivolumab dose groups and between previously treated and treatment-naïve patients (p>0.01 for interaction between time and dose group or previous treatment status). Results of analysis for pharmacodynamic transcriptional effects that differ between treatment groups are presented in Table 7 and Table 8, above. Consistent with the efficacy and IHC results described above, this analysis of gene expression did not identify a large effect of dose or previous treatment.

An analysis of the association between gene expression and Response to nivolumab was performed, with evaluable data for 69 patients. 54 patients had <20% reduction in tumor burden (N=43 at baseline and 44 at cycle 2 day 8 with 33 patients having matched samples) and 15 patients had a ≥20% reduction in tumor burden (N=13 at baseline and 11 at cycle 2 day 8, with 9 patients having matched samples). In the gene expression data obtained at baseline, 311 transcripts were found to be differentially expressed (P<0.01, >1.3× difference, and a false discovery rate <16%) in patients who displayed a ≥20% reduction in tumor burden as compared to those patients with a <20% reduction in tumor burden (FIG. 8A, Table 4). Genes observed to have lower expression levels in those patients with a ≥20% reduction in tumor burden included several involved in establishment of protein localization (P<10⁻⁵), negative regulation of epithelial cell proliferation involved in lung morphogenesis (P<10⁻⁴), and genes previously identified to be downregulated by ipilimumab in melanoma (P<10⁻⁴; see, e.g., Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31). Genes with higher expression levels included several upregulated by ipilimumab in melanoma (P<10⁻²³; see, e.g., Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31), various immune system genes (P<10⁻⁷; 45 genes, e.g., IL15RA, IL1R2, and IRF1), including known myeloid lineage genes (e.g., IL1A, LINC00158, PRAM1, and SPI1), and known lymphoid lineage genes (e.g., CD3E, AIM2, GZMB, NKG7, CD7, and CTSW). In particular, the baseline expression levels of MICB, PVRIG NKG7, SPI1 and CLEC2B were significantly higher in patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction.

In the gene expression data obtained on treatment at Cycle 2 day 8, a total of 779 genes were found to be differentially expressed (P<0.01, >1.3-fold difference, and a false discovery rate <16%) in patients who displayed a ≥20% reduction in tumor burden as compared to those patients with ≤20% reduction (FIG. 8B, Table 5). Genes observed to have lower expression levels in those patients with a ≥20% reduction in tumor burden included an over-representation of cellular component organization genes (P<10⁻¹⁸), signaling genes (P<10⁻¹⁶), and genes previously identified to be downregulated by ipilimumab in melanoma (P<10⁻⁵; see, e.g., Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31). Genes with higher expression levels included over-representation of those upregulated by ipilimumab in melanoma (P<10⁻¹³⁵; see, e.g., Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31), various immune system genes (P<10⁻⁸²; 188 genes), known myeloid lineage genes (51 genes, e.g., CD68, CD86, CASP1, and CSF3R), known lymphoid lineage genes (more than 65 genes, e.g., TCRα/β, CD3D, CD8A, and CD28), cytolytic function genes (e.g., KLRG1, granzymes, and PRF1), interferon regulated genes (24 genes, e.g., AIM2, CASP1, CCL8, and IRF9), and immune checkpoint molecules (e.g., TIGIT, CTLA-4, PD-L2, and IL10RA). In particular, the on treatment expression levels of [ ] CTLA4, PD-L2 (PDCD1LG2), TIGIT, PVRIG, NKG7, SPI1, CLEC2B, CD244, NKTR, TNFSF8, TNFSF13B and TNFRSF14 were significantly higher in patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction (see, e.g., FIG. 8C-FIG. 8E). Note that PVRIG, NKG7, SPI1, CLEC2B are also among the 311 genes differentially expressed at baseline in patients who displayed a ≥20% reduction in tumor burden. Also, NKTR and TNFSF8, are among the subset (from the 779 genes) of 56 genes that also showed >1.25-fold change in expression upon treatment in patients who displayed a ≥20% reduction in tumor burden, with that change upon treatment being significantly different (P<0.01) from any change upon treatment in those patients with <20% reduction.

G. Interferon-γ-Related Chemokines

As the observed increases in interferon-γ-regulated chemokine transcripts in tumor could potentially result in an increase in circulating chemokines in the periphery, serum levels of a number of serum-soluble factors were quantified (Table 12). FIG. 9A and FIG. 9B summarize overall survival as a function of levels of select serum chemokines at baseline, and as a function of the corresponding changes from baseline. In serum, increases were noted in CXCL9 (MIG) and CXCL10 (IP-10), with median changes of 1861 pg/ml (range, −2,000 to 22,890) and 157 (range, −398 to 3.930), respectively, from baseline to cycle 2 day 8 (N=85). Median percent change from baseline of these chemokines were 90% (range, −451% to 1,730%) and 37% (range, −30% to 936%), respectively. Most patients had increases in both CXCL9 and CXCL10 and these increases were observed across all baseline values (FIG. 9C and FIG. 9D). Within-patient changes in CXCL9 (FIG. 9E) tended to be greater than within-patient changes in CXCL10 (FIG. 9H). Changes between CXCL9 and CXCL10 were highly associated (FIG. 9F and FIG. 9G). In tumor, mean levels of CXCL9 (FIG. 9J) and CXCL10 (FIG. 9K) transcripts increased from baseline to cycle 2 day 8 (2.4-fold for 4283 at/CXCL9, p=0.0008 [FIG. 9G]; 2-fold for 3627 at/CXCL10, p=0.011 [FIG. 9K]). These observed changes were not associated with nivolumab dose or previous treatment status (data not shown). At cycle 2 day 8, serum levels of CXCL9 and CXCL10 were associated with their mRNA transcript levels obtained from a corresponding biopsy from the same patient (Partial correlation 0.369 for CXCL9, p=0.006 [FIG. 9L]; Partial correlation 0.298 for CXCL10, p=0.029 [FIG. 9M]).

TABLE 12 List of Serum-soluble Factors Quantified Stem cell factor Vascular epithelial growth factor-3 Brain-derived neurotrophic factor Vascular epithelial growth factor Vascular epithelial growth factor-2 RANTES Vitamin D binding protein Von Willebrand factor α-2 macroglobulin ICAM-1 MCP-1 (CCL2) α-1 antitrypsin CXCL 10 (IP10) VCAM-1 Eotaxin TNF RII Haptoglobin TIMP-1 Ferritin IL2-RA MMP-3 C reactive protein IL-18 Factor VII β-2-microglobulin Complement 3 CXCL9 (MIG) MIP-1 β (CCL4)

H. T-Cell Receptor

T-cell sequencing was used to determine the T-cell receptor (TCR) repertoire in patients pre- and on treatment with nivolumab (FIG. 10A-FIG. 10C). Tumor T-cell frequency increased from an average log (HR) score of about −0.75 pre-treatment to about −0.4 on treatment, with an increased hazard ration (95% CI) from 0.5 (0.2, 0.9) to 0.7 (0.3, 1.3) (FIG. 10D). Tumor clonality of T-cells increased from an average log (HR) score of about −0.5 pre-treatment to about −0.3 on treatment, with a decreased hazard ration (95% CI) from 0.7 (0.3, 1.2) to 0.8 (0.5, 1.4) (FIG. 10E). Blood clonality of T-cells decreased from an average log (HR) score of about 0.2 to 0.1, with a decreased hazard ration (95% CI) from 1.2 (0.8, 1.7) to 1.1 (0.8, 1.6) (FIG. 10F).

IV. Discussion

This is the first translational study involving analysis of both pretreatment and on-treatment biopsies aimed specifically at understanding the immunomodulatory activity of an anti-PD-1 antagonist, e.g., nivolumab, seeking to identify cellular signals associated with T cell reactivation in mRCC. Nivolumab demonstrated an immunomodulatory effect of PD-1 inhibition through multiple lines of evidence across all doses studied.

Clinical activity was observed in both treatment-naïve and previously treated patients at each dose. Median OS was 16.4-25.2 months for previously treated patients, similar to that seen in another recent randomized dose-ranging phase 2 study of nivolumab (Motzer et al. (2014) J Clin Oncol 33:1430-37). Median OS was not reached for treatment-naïve patients.

The IHC analysis of tumor-associated lymphocyte markers (i.e., CD3+, CD4+, CD8+) showed increased lymphocytic presence in biopsies at cycle 2 day 8 of treatment. These data suggest that nivolumab either increased the tumor trafficking or infiltration of T cells in post-treatment biopsies, facilitated the expansion of T cells already within the tumor microenvironment, or both. A recent study examining mutations and response in lung cancer showed that specific CD8+ T cell responses to the anti-PD-1 therapy pembrolizumab paralleled tumor regression (Rizvi et al. (2015) Science 348:124-28), suggesting that the observed increases in tumor-associated lymphocytes could contribute to the clinical effects of nivolumab. Furthermore, a study in metastatic melanoma showed immune infiltrates only in pembrolizumab responders (Tumeh et al. (2014) Nature 515:568-71). The results from the current nivolumab biomarker study in mRCC are not consistent with these findings in melanoma, potentially due to a difference in tumor biology. In the current nivolumab study, some level of induction of tumor-associated lymphocytes was noted in the majority of patients on study across all nivolumab doses.

Nivolumab demonstrated high, sustained PD-1 receptor occupancy on circulating T cells from baseline to cycle 8 day 1 at all dose levels, with no notable differences between previously treated and treatment-naïve patients. Even 0.3 mg/kg nivolumab was sufficient to achieve near-complete saturation of the PD-1 receptor in previously treated patients (>90%). This was higher than the PD-1 receptor occupancy reported in a recent nivolumab study (median, 64%-70%) for a mixed population of patients with various solid tumors (Topalian et al. (2012) N Engl J Med 366:2443-54), suggesting either potential differences between patients with different solid tumors or variations between techniques.

There was a lack of concordance in PD-L1 expression in the fresh and archived samples. In this nivolumab study, objective responses appeared to be more frequent in patients whose fresh biopsies showed ≥5% PD-L1 expression, similar to findings from another study in patients with RCC (Motzer et al. (2014) J Clin Oncol 33:1430-37). Archived samples were typically obtained from patients at diagnosis, suggesting that the tumor biology may change over time and that association with clinical response may be better assessed in samples taken proximal to the latest treatment. Clinical responses to PD-L1 blockade have been observed in patients with tumors expressing high levels of PD-L1, especially when PD-L1 was expressed by tumor-associated lymphocytes (Herbst et al. (2014) Nature 515:563-67). Several patients in the present study classified as showing <5% PD-L1 expression demonstrated objective responses to nivolumab. This is consistent with data previously reported in RCC (Motzer et al. (2014) J Clin Oncol 33:1430-37), melanoma (Robert et al. (2015) N Engl J Med 372:320-30), and squamous cell non-small-cell lung cancer (Carbone et al. (2014) J Clin Oncol 32:Abstract TPS8128). Recognition of the tumor by T cells during the adaptive immune response mediates interferon-γ production and release. Thus, nivolumab-induced T cell reactivation was expected to increase interferon-γ-regulated transcripts and proteins in tumors and potentially elsewhere. Using gene expression profiling in tumor biopsies, interferon-γ transcripts and interferon-regulated transcripts were found to have increased in tumors, while only interferon-regulated transcripts rapidly and transiently increase in whole blood following nivolumab treatment. Transcripts for T cell receptor subunits (CD3γ, TCRα, TCRβ) rapidly and transiently decreased in whole blood after treatment with nivolumab, suggesting that treatment with nivolumab may prompt T cells to exit the periphery. These effects in the blood were concurrent with a transient decrease in levels of CD27 transcript, an immune cell marker important for long-term maintenance of T cell immunity (DeBarros et al. (2011) Eur J Immunol 41:195-201). In tumor biopsies, expression of genes from lymphoid- and myeloid-specific lineages was elevated at cycle 2 day 8 of study treatment, indicating that both cell types have an increased presence upon treatment. These effects are in line with observations from previous studies that demonstrated enhanced T cell activation and increased expression of interferon-γ at the tumor site, resulting from PD-L1/PD-L2 blockade or PD-1 inhibition (Brown et al. (2003) J Immunol 170:1257-66; Rodig et al. (2003) Eur J Immunol 33:3117-26; Peng et al. (2012) Cancer Res 72:5209-18).

Chemokines are known to guide the trafficking behavior of T cells as part of the immune response against tumors. In this study, increased transcription of genes for the key chemokines CXCL9 and CXCL10 at the tumor site was observed following treatment with nivolumab, potentially induced through interferon-γ production. Furthermore, high serum concentrations of CXCL9 and CXCL10 at cycle 2 day 8, in the absence of their transcripts in whole blood at cycle 1 day 2 or cycle 2 day 8, suggest that the tumor is the source of these chemoattractants (Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31). Nearly all patients on study showed some induction of these chemokines. These findings were consistent with the transcriptional changes in the tumor and peripheral blood.

The type and frequency of AEs were similar in both previously treated and treatment-naïve patients, and the pattern and type of AEs were also consistent with previous reports of nivolumab in mRCC, advanced metastatic melanoma, colorectal cancer, castrate-resistant prostate cancer, and non-small-cell lung cancer (Brahmer et al. (2010) J Clin Oncol 28:3167-75; Drake et al. (2013) J Clin Oncol 31:Abstract 4514; Motzer et al. (2014) J Clin Oncol 33:1430-37). There was no obvious dose-dependent relationship, and the rate of severe AEs was low. Overall, nivolumab was well tolerated.

Nivolumab monotherapy demonstrated immunomodulation consistent with PD-1 inhibition in the majority of patients, as evidenced by serial analysis of tumor-associated lymphocytes, genome-wide RNA profiling, and analysis of chemokines and related cell markers. The analysis of the tumor microenvironment in pretreatment versus on-treatment patient biopsies afforded key insights beyond the scope of xenograft models and the limited number of biomarker studies that exist for anti-PD-1 therapies in mRCC, which used only pretreatment biopsies to evaluate treatment responses. These on-treatment changes in tumor and peripheral blood gene expression and serum immune markers were not dose dependent and were similar between previously treated and treatment-naïve patients. In particular, data presented here and elsewhere continue to point to the critical role of Th1 response factors such as CXCL9 and CXCL10 in the anti-tumor activity observed with checkpoint inhibitors (Ji et al. (2012) Cancer Immunol. Immunother. 61:1019-31). This study also adds to the growing evidence that nivolumab is effective in tumors regardless of PD-L1 expression.

The genes provided in Tables 6, 7, and 8 suggest mechanistic hypotheses for sensitivity to nivolumab therapy involving the presence of both myeloid and lymphoid cell types, and their interaction. In patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction, an increased presence of NK cells is indicated by transcripts including PVRIG and NKG7 (at baseline) and PVRIG, TIGIT, NKG7, NKTR and CD244 (upon treatment), and an increased presence of myeloid cells is indicated by transcripts including SPI1 and CLEC2B (at baseline and on treatment).

One mechanism of sensitivity may involve differential activation of the cytolytic response of NK and NKT cells. Prior to therapy, MICB and CLEC2B transcripts are elevated in RCC patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction. Enhanced tumor expression of ligands that bind the NKG2D/KLRK1 receptor (i.e. MICB, MICA, RAET1E, RAET1G, ULBP2, ULBP1, RAET1L, and ULBP3) or NKp80/KLRF1 (i.e. CLEC2B) would enhance NK cell cytolytic activity. Upon therapy, NKTR, CD244, TNFRSF14, PVRIG and TIGIT transcripts are elevated in RCC patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction. NKTR and CD244 proteins are considered likely to positively modulate the cytolytic activity triggered by nivolumab, TNFRSF14 has both inhibitory and activating roles, whereas PVRIG and TIGIT are considered to be co-inhibitory receptors and in this context the latter may serve in the feedback inhibition that ultimately controls the immune response unleashed by nivolumab.

Another mechanism of sensitivity may involve differential effects upon adaptive immunity. Upon therapy, TNFSF8 and TNFSF13B transcripts are elevated in RCC patients exhibiting a ≥20% reduction in tumor burden as compared to those with <20% reduction. TNFSF13B/BAFF plays an important role in the proliferation and differentiation of B cells, and engagement of TNFSF8 expressed by human IgD-positive IgM-positive B cells was reported to inhibit class switch DNA recombination and antibody production.

Another mechanism of sensitivity may involve differential effects on antigen presentation. We have noted increased transcripts for 12 proteins involved in Class I antigen presentation among the 108 genes significantly regulated by nivolumab treatment (Table 2; FIG. 7B). Responders to nivolumab therapy may posses intrinsic differences in number or type of antigenic peptides available for presentation through Class I (e.g. neo-epitopes arising from mutational burden of their tumor), and this may further intersect with components represented in Table 6A and Table 7A. 

1. A method for treating a subject afflicted with a tumor derived from a renal cell carcinoma (RCC) comprising: (i) administering to the subject a first dose of an antibody or an antigen-binding portion thereof that binds specifically to a Programmed Death-1 receptor (PD-1) and inhibits PD-1 activity (“anti-PD-1 antibody”) or an antibody or an antigen-binding portion thereof that binds specifically to a Programmed Death-Ligand 1 (PD-L1) and inhibits PD-L1 activity (“anti-PD-L1 antibody”), respectively; and (ii) administering a second dose of the anti-PD-1 antibody or the anti-PD-L1 antibody to the subject wherein after the administration of the first dose, the subject exhibits differential expression of cytotoxic T-lymphocyte antigen (“CTLA-4”), T-cell immunoreceptor with Ig and ITIM domains (“TIGIT”), Programmed Death-Ligand 2 (“PD-L2”), or any combination thereof. 2-60. (canceled)
 61. A method for identifying a subject afflicted with a tumor who is suitable for an anti-PD-1 antibody or an anti-PD-L1 antibody therapy, comprising measuring an expression level of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof in a sample of the subject prior to the anti-PD-1 antibody or anti-PD-L1 antibody therapy, wherein the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, and wherein the subject is administered a first dose of an anti-PD-1 antibody or an anti-PD-L1 antibody.
 62. A method for treating a subject afflicted with a tumor comprising administering to the subject who exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to a reference expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7, a first dose of an anti-PD-1 antibody or an anti-PD-L1 antibody. 63-65. (canceled)
 66. The method of claim 61, wherein the subject exhibits differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after the administration of the first dose of the anti-PD-1 antibody or the anti-PD-L1 antibody.
 67. The method of claim 66, wherein: (i) the differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof is relative to the expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 prior to the administration of the first dose; or (ii) the differential expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof is relative to the expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 non-responders.
 68. (canceled)
 69. The method of claim 66, further comprising administering a second dose of an anti-PD-1 antibody or an anti-PD-L1 antibody to the subject, wherein the subject exhibits a differential expression level of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, and/or PD-L2 prior to the administration of the first dose.
 70. The method of claim 66, wherein the subject exhibits increased expression of PVRIG, NKG7, CD244, NKTR, TNFSF8, TNFSF13B, TNFRSF14, SPI1, CLEC2B, CTLA-4, TIGIT, PD-L2, or any combination thereof after the administration of the first dose.
 71. The method of claim 61, wherein after the administration of the first dose, the subject further exhibits a characteristic selected from the group consisting of: (i) an increased expression of one or more serum markers of Interferon-γ activation; (ii) an increased tumor gene expression; (iii) a decreased clonality of T cell Receptor in serum; (iv) an increased T cell count in the tumor; and (v) any combination thereof.
 72. (canceled)
 73. The method of claim 61, wherein: (i) the expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is a protein expression measured by an immunohistochemistry, an ELISA, a western blot, a protein array or any combination thereof; or (ii) the expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof is a nucleotide expression measured by an in situ hybridization, a DNA or RNA array or nucleotide hybridization technique, a tumor sequencing technique, a quantitative polymerase chain reaction (PCR), or any combination thereof. 74-79. (canceled)
 80. The method of claim 61, wherein the anti-PD-1 antibody is nivolumab or pembrolizumab. 81-84. (canceled)
 85. The method of claim 61, wherein the anti-PD-L1 antibody is BMS-936559, MPDL3280A, MEDI4736, or MSB0010718C. 86-89. (canceled)
 90. The method of claim 62, wherein the first dose of the anti-PD-1 antibody is administered at a flat dose of at least about 240 mg or at least about 480 mg.
 91. The method of claim 62, wherein the first dose of the anti-PD-1 antibody is administered at a flat dose of at least about 240 mg once about every 2 weeks or a flat dose of at least about 480 mg once about every 4 weeks. 92-95. (canceled)
 96. The method of claim 62, which further comprises administering one or more additional anti-cancer agents.
 97. The method of claim 96, wherein the anti-cancer agent is selected from the group consisting of an antibody or antigen-binding portion thereof that binds specifically to CTLA-4 (“anti-CTLA-4 antibody”) and inhibits CTLA-4 activity, a chemotherapy, a platinum-based doublet chemotherapy, a tyrosine kinase inhibitor, an anti-VEGF inhibitor, or any combination thereof.
 98. (canceled)
 99. The method of claim 97, wherein the anti-cancer agent is ipilimumab.
 100. The method of claim 61, wherein the tumor is a Renal Cell Carcinoma.
 101. A kit for treating a subject afflicted with a tumor, the kit comprising: (a) an anti-PD-1 antibody or an anti-PD-L1 antibody; and (b) instructions for determining differential expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof and for administering a first dose of the anti-PD-1 antibody or the anti-PD-L1 antibody in the method of claim 61 if the subject exhibits increased expression of MICB, PVRIG, SPI1, CLEC2B, NKG7, or any combination thereof, relative to an average expression level of MICB, PVRIG, SPI1, CLEC2B, and/or NKG7.
 102. (canceled)
 103. The method of claim 97, wherein the first dose of the anti-PD-1 antibody is administered at a dose of about 1 mg/kg body weight once about every three weeks.
 104. The method of claim 62, wherein the first dose of the anti-PD-L1 antibody is administered at a flat dose of at least about 1200 mg. 